Geolocation of unpublished archaeological sites in the Peruvian Amazon

Published maps identifying archaeological sites in the Amazon basin show a paucity of sites in western Amazonia compared to the Brazilian Amazon. Whereas fewer than two dozen are identified for the Peruvian Amazon on basin-wide maps, a thorough review of unpublished archival material held by the Ministry of Culture of Peru and other sources revealed more than 400 known but unpublished sites in the Department of Loreto, challenging the notion that the region was sparsely occupied in prehistory. Our database provides the geolocation of each site and corresponding references for use by scientists seeking to better understand regional Pre-Columbian human occupation and settlement, cultural change, resource use and their landscape legacies. These data are foundational not only to the development of a richer understanding of prehistory and historical ecology of the Amazon basin but importantly for informing current land use, forest conservation and development policies as well as initiatives to support indigenous land and cultural rights in Amazonia.

Measurement(s)	archaeological site • geographic location
Technology Type(s)	digital curation
Sample Characteristic - Location	Amazon Basin

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.16750639

Historical Ecology in Brazil: A Systematic Mapping of Scientific Articles (1998–2021)

Historical Ecology is a multidisciplinary field that studies long-term relationships between humanity and the environment. There is a missing synthesis effort to organize and present the state of the scholarship in Historical Ecology in Brazil. We aimed to characterize by whom, when, where, what, and how research in Historical Ecology has been conducted in Brazil. We made a systematic mapping of 118 scientific articles published in Portuguese, Spanish, and English that fit our inclusion criteria. The results showed articles from 1998 to May 2021, published in 79 different journals. We found 264 national and international authors (60% men and 40%women); 91% of all investigations were carried out in the Amazon and Atlantic Forest biomes. There are few works about Cerrado, Caatinga, and Pampa, and none for Pantanal. The most mentioned keywords were historical ecology, Amazon, forest, and archaeology. Twenty-three articles focused on a particular species, primarily plants; 37% of all articles used Historical Ecology as its central axis of research, and 63% as auxiliary. We found more than 35 methodological procedures, both from the social and natural sciences. This overview revealed achievements, research gaps, and opportunities in this field.

Theoretical Clues for Agroecological Transitions: The Conuco Legacy and the Monoculture Trap

The multiple ecological crisis that we are facing forces us to ponder the transition toward sustainable agricultural systems. Two key uncertainties need to be unveiled in addressing this problem; first, we need to identify the general features of alternative models that make them sustainable, and second, we need to explore how to build them from the (flawed) existing systems. In this work we explore these two questions using an ethnoecological and theoretical approach. In the exploration of alternative models, we evaluate an ancestral farming system, the conuco, characterized by, (i) the use of the ecological succession to constantly renew its properties, (ii) the increase of its biodiversity over time (in the horizontal and vertical components), and (iii) the self-regulation of the associated populations. Next, we characterize the topology of ecological networks of agroecosystems along the transition from a monoculture to a conuco-like agroecological system. We use topologies obtained from field information of conventional and agroecological systems as starting and arrival points. To model the dynamics of the systems and numerically simulate the transitions, we use a model based on Generalized Lotka-Volterra equations, where all types of population interactions are represented, with outcomes based on a density-dependent conditionality. The results highlight the relevance of increasing the connectance and diminishing the degree centrality of the conventional systems networks to promote their sustainability. Finally, we propose that the transitions between the monoculture and the agroecological systems could be figuratively interpreted as a cusp catastrophe, where the two systems are understood as alternative stable states and the path from one to the other cannot be reverted by just reversing the values of the control parameter. That is, once a system is in either of these states there is a tendency to stay and a resistance to move away from it. This implies that in the process of transition from a monoculture to a multi-diverse system, it is prudent not to despair if there are no immediate improvements in the performance of the system because once a certain point is reached, the system may experience an abrupt improvement.

Looking into the flora of Dutch Brazil: botanical identifications of seventeenth century plant illustrations in the Libri Picturati

The Libri Picturati includes a collection of plant illustrations from seventeenth century Dutch Brazil that is kept in the Jagiellonian library in Krakow since World War II. While many studies focused on the artistic details and history of these images, we identified the flora depicted. We used contemporary textual sources (e.g., Historia Naturalis Brasiliae), monographs and taxonomist' assessments. We checked origin, life form, domestication and conservation status and the plant parts that are represented. We identified 198 taxa, consisting mostly of wild, native rainforest trees and 35 introduced species. Fertile branches are the most represented, although some loose dry fruits and sterile material were also painted, which sheds light into the collection methods by naturalists in Dutch Brazil. Several species are no longer abundant or have become invasive due to anthropogenic influences since colonialism. Through this botanical iconography, we traced the first records of the sunflower and the Ethiopian pepper in Brazil, as well as the dispersion and assimilation of the flora encountered in the colony by Indigenous, African and European peoples. We emphasized the relevance of combining visual and textual sources when studying natural history collections and we highlighted how digitalization makes these artistic and scientific collections more accessible.

A 5,000-year vegetation and fire history for tierra firme forests in the Medio Putumayo-Algodón watersheds, northeastern Peru

This paper addresses an important debate in Amazonian studies; namely, the scale, intensity, and nature of human modification of the forests in prehistory. Phytolith and charcoal analysis of terrestrial soils underneath mature tierra firme (nonflooded, nonriverine) forests in the remote Medio Putumayo-Algodón watersheds, northeastern Peru, provide a vegetation and fire history spanning at least the past 5,000 y. A tree inventory carried out in the region enables calibration of ancient phytolith records with standing vegetation and estimates of palm species densities on the landscape through time. Phytolith records show no evidence for forest clearing or agriculture with major annual seed and root crops. Frequencies of important economic palms such as Oenocarpus, Euterpe, Bactris, and Astrocaryum spp., some of which contain hyperdominant species in the modern flora, do not increase through prehistoric time. This indicates pre-Columbian occupations, if documented in the region with future research, did not significantly increase the abundance of those species through management or cultivation. Phytoliths from other arboreal and woody species similarly reflect a stable forest structure and diversity throughout the records. Charcoal 14C dates evidence local forest burning between ca. 2,800 and 1,400 y ago. Our data support previous research indicating that considerable areas of some Amazonian tierra firme forests were not significantly impacted by human activities during the prehistoric era. Rather, it appears that over the last 5,000 y, indigenous populations in this region coexisted with, and helped maintain, large expanses of relatively unmodified forest, as they continue to do today.

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.

Adaptive management strategies of local communities in two Amazonian floodplain ecosystems in the face of extreme climate events

In Amazonia, changes in the frequency and intensity of extreme climate events are occurring and expected to intensify, affecting food security with subsequent social and political problems. We conducted semi-structured interviews in communities of the mid-Solimões River basin (Amazonas, Brazil). Our questions were designed to construct seasonal calendars with residents (ribeirinhos) to understand climatic patterns and changes in livelihood activities, how traditional management is affected by extreme floods and droughts, and to identify their adaptation strategies in new climatic contexts. We studied three floodplain (várzea, n = 59 households) and three paleo-floodplain communities, situated 1-3 m higher than the floodplain (paleovárzea, n = 42 households). We show that these local communities have detailed knowledge of climate patterns and changes, and that they recognize that climatic unpredictability hinders effective planning of subsistence activities, because their local knowledge is no longer fully reliable. Extreme climate events have consequences for their farming systems and associated agrobiodiversity, varying according to the degree of exposure of different environments to extreme events. During extreme events ribeirinhos intensify adaptation strategies, such as avoiding stress to fruit-tree root systems, prioritizing plants that survive flooding and working in less affected landscapes. Adaptation practices with long histories tend to occur more often in floodplains, and two adaptation practices were specific to floodplains. The impacts of extreme events on local communities are expected to increase, especially in environments more exposed to floods. Local residents suggest the documentation and sharing of adaptation strategies as a way to increase their resilience.

Eighty-four per cent of all Amazonian arboreal plant individuals are useful to humans

Plants have been used in Amazonian forests for millennia and some of these plants are disproportionally abundant (hyperdominant). At local scales, people generally use the most abundant plants, which may be abundant as the result of management of indigenous peoples and local communities. However, it is unknown whether plant use is also associated with abundance at larger scales. We used the population sizes of 4,454 arboreal species (trees and palms) estimated from 1946 forest plots and compiled information about uses from 29 Amazonian ethnobotany books and articles published between 1926 and 2013 to investigate the relationship between species usefulness and their population sizes, and how this relationship is influenced by the degree of domestication of arboreal species across Amazonia. We found that half of the arboreal species (2,253) are useful to humans, which represents 84% of the estimated individuals in Amazonian forests. Useful species have mean populations sizes six times larger than non-useful species, and their abundance is related with the probability of usefulness. Incipiently domesticated species are the most abundant. Population size was weakly related to specific uses, but strongly related with the multiplicity of uses. This study highlights the enormous usefulness of Amazonian arboreal species for local peoples. Our findings support the hypothesis that the most abundant plant species have a greater chance to be useful at both local and larger scales, and suggest that although people use the most abundant plants, indigenous people and local communities have contributed to plant abundance through long-term management.

A "Dirty" Footprint: Macroinvertebrate diversity in Amazonian Anthropic Soils

Amazonian rainforests, once thought to be pristine wilderness, are increasingly known to have been widely inhabited, modified, and managed prior to European arrival, by human populations with diverse cultural backgrounds. Amazonian Dark Earths (ADEs) are fertile soils found throughout the Amazon Basin, created by pre-Columbian societies with sedentary habits. Much is known about the chemistry of these soils, yet their zoology has been neglected. Hence, we characterized soil fertility, macroinvertebrate communities, and their activity at nine archeological sites in three Amazonian regions in ADEs and adjacent reference soils under native forest (young and old) and agricultural systems. We found 673 morphospecies and, despite similar richness in ADEs (385 spp.) and reference soils (399 spp.), we identified a tenacious pre-Columbian footprint, with 49% of morphospecies found exclusively in ADEs. Termite and total macroinvertebrate abundance were higher in reference soils, while soil fertility and macroinvertebrate activity were higher in the ADEs, and associated with larger earthworm quantities and biomass. We show that ADE habitats have a unique pool of species, but that modern land use of ADEs decreases their populations, diversity, and contributions to soil functioning. These findings support the idea that humans created and sustained high-fertility ecosystems that persist today, altering biodiversity patterns in Amazonia.

Decoloniality and anti-oppressive practices for a more ethical ecology

Ecological research and practice are crucial to understanding and guiding more positive relationships between people and ecosystems. However, ecology as a discipline and the diversity of those who call themselves ecologists have also been shaped and held back by often exclusionary Western approaches to knowing and doing ecology. To overcome these historical constraints and to make ecology inclusive of the diverse peoples inhabiting Earth's varied ecosystems, ecologists must expand their knowledge, both in theory and practice, to incorporate varied perspectives, approaches and interpretations from, with and within the natural environment and across global systems. We outline five shifts that could help to transform academic ecological practice: decolonize your mind; know your histories; decolonize access; decolonize expertise; and practise ethical ecology in inclusive teams. We challenge the discipline to become more inclusive, creative and ethical at a moment when the perils of entrenched thinking have never been clearer.

‘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 role of anthropogenic dispersal in shaping the distribution and genetic composition of a widespread North American tree species

Dispersal and colonization are among the most important ecological processes for species persistence as they allow species to track changing environmental conditions. During the last glacial maximum (LGM), many cold-intolerant Northern Hemisphere plants retreated to southern glacial refugia. During subsequent warming periods, these species expanded their ranges northward. Interestingly, some tree species with limited seed dispersal migrated considerable distances after the LGM ~19,000 years before present (YBP). It has been hypothesized that indigenous peoples may have dispersed valued species, in some cases beyond the southern limits of the Laurentide Ice Sheet. To investigate this question, we employed a molecular genetics approach on a widespread North American understory tree species whose fruit was valued by indigenous peoples. Twenty putative anthropogenic (near pre-Columbian habitations) and 62 wild populations of Asimina triloba (pawpaw), which produces the largest edible fruit of any North American tree, were genetically assayed with nine microsatellite loci. Putative anthropogenic populations were characterized by reduced genetic diversity and greater excess heterozygosity relative to wild populations. Anthropogenic populations in regions that were glaciated during the LGM had profiles consistent with founder effects and reduced gene flow, and shared rare alleles with wild populations hundreds of kilometers away (mean = 723 km). Some of the most compelling evidence for human-mediated dispersal is that putative anthropogenic and wild populations sharing rare alleles were separated by significantly greater distances (mean = 695 km) than wild populations sharing rare alleles (mean = 607 km; p = .014). Collectively, the genetic data suggest that long-distance dispersal played an important role in the distribution of pawpaw and is consistent with the hypothesized role of indigenous peoples.

Shifting cultivation and hunting across the savanna-forest mosaic in the Gran Sabana, Venezuela: facing changes

BACKGROUND

Human encroachment and overexploitation of natural resources in the Neotropics is constantly increasing. Indigenous communities all across the Amazon, are trapped between a population rise and a hot debate about the sustainability of hunting rates. The Garden Hunting hypothesis states that shifting cultivation schemes (conucos) used by Amazon indigenous communities may generate favorable conditions, increasing abundance of small and medium wildlife species close to the 'gardens' providing game for indigenous hunters.

METHODS

Here, we combined camera trap surveys and spatially explicit interview dataset on Pemón indigenous hunting scope and occurrence in a mosaic of savanna and forest in the Gran Sabana, Venezuela to evaluate to what extent the wildlife resource use corresponds to Garden Hunting hypothesis. We applied the Royle-Nichols model and binomial regression in order to: (1) assess whether abundance of small and medium wildlife species is higher close to conucos and (2) evaluate whether hunters select hunting localities based on accessibility to wildlife resources (closeness to conuco) more than wildlife abundance.

RESULTS

We find mixed evidence supporting the Garden Hunting hypothesis predictions. Abundance of small and medium species was high close to conucos but the pattern was not statistically significant for most of them. Pemón seem to hunt in locations dominated by forest, where species abundance was predicted to be higher, than in close vicinity to conucos. Hunting scope was focused on the most abundant species located close to the conuco (Cuniculus paca), but also in less abundant and unavailable species (Crax alector, Tapirus terrestris and Odocoileus virginianus).

CONCLUSIONS

Our research provided the first attempt of a systematic sampling survey in the Gran Sabana, generating a quantitative dataset that not only describes the current pattern of wildlife abundance, but sets the base-line to monitor temporal and spatial change in this region of highland Amazon. We discuss the applicability of the estimates generated as a baseline as well as, environmental challenges imposed by economic, social and cultural changes such as mining encroachment for wildlife management.

Linking Past and Present Land-Use Histories in Southern Amazonas, Peru

This paper analyzes remotely sensed data sources to evaluate land-use history within the Peruvian department of Amazonas and demonstrates the utility of comparing present and past land-use patterns using continuous datasets, as a complement to the often dispersed and discrete data produced by archaeological and paleoecological field studies. We characterize the distribution of ancient (ca. AD 1–1550) terracing based on data drawn from high-resolution satellite imagery and compare it to patterns of deforestation between 2001 and 2019, based on time-series Landsat data. We find that the patterns reflected in these two datasets are statistically different, indicating a distinctive shift in land-use, which we link to the history of Inka and Spanish colonialism and Indigenous depopulation in the 15th through 17th centuries AD as well as the growth of road infrastructure and economic change in the recent past. While there is a statistically significant relationship between areas of ancient terracing and modern-day patterns of deforestation, this relationship ultimately explains little (6%) of the total pattern of modern forest loss, indicating that ancient land-use patterns do not seem to be structuring modern-day trajectories of land-use. Together, these results shed light on the long-term history of land-use in Amazonas and their enduring legacies in the present.

Geographic Patterns of Genetic Variation among Cacao (Theobroma cacao L.) Populations Based on Chloroplast Markers

The cacao tree (Theobroma cacao L.) is native to the Amazon basin and widely cultivated in the tropics to produce seeds, the valuable raw material for the chocolate industry. Conservation of cacao genetic resources and their availability for breeding and production programs are vital for securing cacao supply. However, relatively little is still known about the phylogeographic structure of natural cacao populations. We studied the geographic distribution of cpDNA variation in different populations representing natural cacao stands, cacao farms in Ecuador, and breeding populations. We used six earlier published cacao chloroplast microsatellite markers to genotype 233 cacao samples. In total, 23 chloroplast haplotypes were identified. The highest variation of haplotypes was observed in western Amazonia including geographically restricted haplotypes. Two observed haplotypes were widespread across the Amazon basin suggesting long distance seed dispersal from west to east in Amazonia. Most cacao genetic groups identified earlier using nuclear SSRs are associated with specific chloroplast haplotypes. A single haplotype was common in selections representing cacao plantations in west Ecuador and reference Trinitario accessions. Our results can be used to determine the chloroplast diversity of accessions and in combination with phenotypic assessments can help to select geographically distinctive varieties for cacao breeding programs.

Notes on current Mbyá-Guarani medicinal plant exchanges in southern Brazil

BACKGROUND

Experts in the Atlantic Forest, the Guarani people have the habit of transporting and exchanging plants due to their mobility throughout the territory. Historically, this habit contributed to the species composition and diversification among different phytophysiognomies that comprise the Atlantic Forest. Medicine and spirituality are traits that stand out within the Guarani culture, which is based on a holistic understanding of physical and spiritual well-being for the person's health. To achieve this balance, they use a range of native and adapted plant species. Our goal is to understand some of the Guarani contributions to the cultural landscape in the Atlantic Forest.

METHODS

We conducted semi-structured interviews with key persons asking about the importance of forest environments for Guarani health and about visits to other Guarani villages and plants exchanged. Data analysis was qualitative, and through a bipartite network of exchanged plants to show current plant exchanges between villages.

RESULTS

We visited seven Guarani Indigenous Territories in south Brazil, and with the participation of 12 respondents, we registered 27 species that were exchanged through different phytophysiognomies in the Atlantic Forest. These results show an intense movement of plants currently occurring between villages and the importance of these movements for both individual health and the integrity of the environments in which the Guarani villages are inserted.

CONCLUSIONS

We observed a search for the maintenance of traditional species in the Guarani medical system, and we highlight the fundamental role of Guarani management in the conservation of the southern Atlantic Forest in indigenous territories.

Amazon tree dominance across forest strata

The forests of Amazonia are among the most biodiverse plant communities on Earth. Given the immediate threats posed by climate and land-use change, an improved understanding of how this extraordinary biodiversity is spatially organized is urgently required to develop effective conservation strategies. Most Amazonian tree species are extremely rare but a few are common across the region. Indeed, just 227 'hyperdominant' species account for >50% of all individuals >10 cm diameter at 1.3 m in height. Yet, the degree to which the phenomenon of hyperdominance is sensitive to tree size, the extent to which the composition of dominant species changes with size class and how evolutionary history constrains tree hyperdominance, all remain unknown. Here, we use a large floristic dataset to show that, while hyperdominance is a universal phenomenon across forest strata, different species dominate the forest understory, midstory and canopy. We further find that, although species belonging to a range of phylogenetically dispersed lineages have become hyperdominant in small size classes, hyperdominants in large size classes are restricted to a few lineages. Our results demonstrate that it is essential to consider all forest strata to understand regional patterns of dominance and composition in Amazonia. More generally, through the lens of 654 hyperdominant species, we outline a tractable pathway for understanding the functioning of half of Amazonian forests across vertical strata and geographical locations.

Amazon-derived nutraceuticals: Promises to mitigate chronic inflammatory states and neuroinflammation

Nutraceuticals have been the focus of numerous research in recent years and accumulating data support their use for promoting some health benefits. Several nutraceuticals have been widely studied as supplements due to their functional properties ameliorating symptoms associated with neurological disorders, such as oxidative stress and chronic inflammatory states. This seems to be the case of some fruits and seeds from the Amazon Biome consumed since the pre-Columbian period that could have potential beneficial impact on the human nervous system. The beneficial activities of these food sources are possibly related to a large number of bioactive molecules including polyphenols, carotenoids, unsaturated fatty acids, vitamins, and trace elements. In this context, this review compiled the research on six Amazonian fruits and seeds species and some of the major nutraceuticals found in their composition, presenting brief mechanisms related to their protagonist action in improving inflammatory responses and neuroinflammation.

Mass Mortality as a Way of Structuring Amazonian and Alpine Tree Populations: Evidence After Storm Vaia

By logging in the past, humans can determine current tree population structures, but fast stump decomposition makes difficult to falsify that for Amazonian Rainforests. We reconstructed land-use histories and surveyed trees ≥ 10 cm diameter at breast height on three 1-ha plots (K1, K2, and K6) in Kühbergl, South Tyrolean Alps as we did for four plots in Atacapi, Ecuador (plots A, B, C, and D). Storm Vaia (October 27 –November 1, 2018) stroke Kübergl providing dated evidence of mass tree-mortality on plot K6. We used K6 as control for comparing its pre- and post-storm population structures with the ones of four Amazonian, and three Alpine species where Vaia did not kill trees (Kolmogorov-Smirnov tests). When compared with K6’s Picea abies, the following species had size distributions similar to post-storm, but not to pre-storm situation. Amazonian: Piptocoma discolor, Vochysia bracelineae (plots B and D), Miconia decurrens (plots B and C), and Pseudobombax sp (plot C). Alpine: Larix decidua (plot K1) and Picea abies (plot K2). Storms do not occur in Atacapi, where logging is a common practice. That makes plausible that discrete events of compulsive logging during secondary succession made Amazonian population structures to look similar to K6’s P. abies. Logging is forbidden in Kühbergl, but storms are common there. Thus, the current population structures of Larix decidua (plot K1) and Picea abies (plot K2) should be legacies of storms before Vaia. Looking into tree populations’ history can impulse research for answering some basic questions of Ecology: what alters population structures, and which population structuring processes are more influential than others.

Reimagining the relationship between Gondwanan forests and Aboriginal land management in Australia's "Wet Tropics"

The "Wet Tropics" of Australia host a unique variety of plant lineages that trace their origins to the super-continent of Gondwanaland. While these "ancient" evolutionary records are rightly emphasized in current management of the region, multidisciplinary research and lobbying by Rainforest Aboriginal Peoples have also demonstrated the significance of the cultural heritage of the "Wet Tropics." Here, we evaluate the existing archeological, paleoenvironmental, and historical evidence to demonstrate the diverse ways in which these forests are globally significant, not only for their ecological heritage but also for their preservation of traces of millennia of anthropogenic activities, including active burning and food tree manipulation. We argue that detailed paleoecological, ethnobotanical, and archeological studies, working within the framework of growing national and world heritage initiatives and active application of traditional knowledge, offer the best opportunities for sustainable management of these unique environments in the face of increasingly catastrophic climate change and bushfires.

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.

Holocene land and sea-trade routes explain complex patterns of pre-Columbian crop dispersion

Pre-Columbian crop movement remains poorly understood, hampering a good interpretation of the domestication and diversification of Neotropical crops. To provide new insights into pre-Columbian crop movement, we applied spatial genetics to identify and compare dispersal routes of three American crops between Mesoamerica and the Andes, two important centres of pre-Columbian crop and cultural diversity. Our analysis included georeferenced simple-sequence repeats (SSR) marker datasets of 1852 genotypes of cherimoya (Annona cherimola Mill.), a perennial fruit crop that became underutilised in the Americas after the European conquest, 770 genotypes of maize (Zea mays L.) and 476 genotypes of common bean (Phaseolus vulgaris L.). Our findings show that humans brought cherimoya from Mesoamerica to present Peru through long-distance sea-trade routes across the Pacific Ocean at least 4700 yr bp, after more ancient dispersion of maize and other crops through the Mesoamerican isthmus over land and near-coastal waters. To our knowledge, this is the first evidence of pre-Columbian crop movement between Mesoamerica and the Andes across the Pacific Ocean providing new insights into pre-Columbian crop exchange in the Americas. We propose that cherimoya represents a wider group of perennial fruit crops dispersed by humans via sea-trade routes between Mesoamerica and the Andes across the Pacific Ocean.

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.

Re-imagining environmental governance: Gold dredge mining vs Territorial Health in the Colombian Amazon

This article describes and analyses an encounter in the Colombian Amazon between Indigenous practices and arrangements to manage their environment and the conservation policies of the State. Indigenous peoples understand their world as populated by powerful human and nonhuman beings; for them, the moral duty of achieving happiness and abundance for all implies sustaining reciprocal and respectful relations with these beings (including the State). In contrast Colombian environmental policy distinguishes between nature and culture, seeking to safeguard landscapes from human interference so that natural processes can unfold unhindered. In practice these partially connected, yet incommensurable worldviews make for a 'perfect storm' - opening opportunities for illegal mining. Drawing on recent fieldwork among the Andoke, an ethnic group well acquainted with extractivism in its different historical modalities and presently affronting the fallout of gold dredge mining we narrate how a parallel, non-state governance system makes it difficult for them to care for their land and entertain mutual and respectful relations with human and nonhuman beings (which we translate as 'territorial health'). We conclude by arguing for the need to re-imagine environmental governance in ways that more closely engage with what we call pluriversal governance: a form of (environmental) governance that does ontological justice to those involved in the environmental conflict - including, crucially, Indigenous people.

Investigating Biotic Interactions in Deep Time

Recent renewed interest in using fossil data to understand how biotic interactions have shaped the evolution of life is challenging the widely held assumption that long-term climate changes are the primary drivers of biodiversity change. New approaches go beyond traditional richness and co-occurrence studies to explicitly model biotic interactions using data on fossil and modern biodiversity. Important developments in three primary areas of research include analysis of (i) macroevolutionary rates, (ii) the impacts of and recovery from extinction events, and (iii) how humans (Homo sapiens) affected interactions among non-human species. We present multiple lines of evidence for an important and measurable role of biotic interactions in shaping the evolution of communities and lineages on long timescales.

Stable isotope evidence for dietary diversification in the pre-Columbian Amazon

Archaeological research is radically transforming the view that the Amazon basin and surrounding areas witnessed limited societal development before European contact. Nevertheless, uncertainty remains on the nature of the subsistence systems and the role that aquatic resources, terrestrial mammalian game, and plants had in supporting population growth, geographic dispersal, cultural adaptations and political complexity during the later stages of the pre-Columbian era. This is exacerbated by the general paucity of archaeological human remains enabling individual dietary reconstructions. Here we use stable carbon and nitrogen isotope analysis of bone collagen to reconstruct the diets of human individuals from São Luís Island (Brazilian Amazon coast) dated between ca. 1800 and 1000 cal BP and associated with distinct ceramic traditions. We expanded our analysis to include previously published data from Maracá and Marajó Island, in the eastern Amazon. Quantitative estimates of the caloric contributions from food groups and their relative nutrients using a Bayesian Mixing Model revealed distinct subsistence strategies, consisting predominantly of plants and terrestrial mammals and variably complemented with aquatic resources. This study offers novel quantitative information on the extent distinct food categories of polyculture agroforestry systems fulfilled the caloric and protein requirements of Late Holocene pre-Columbian populations in the Amazon basin.

Reframing the Wilderness Concept can Bolster Collaborative Conservation

Indigenous territories represent ~45% of land categorized as wilderness in the Amazon, but account for <15% of all forest loss on this land. At a time when the Amazon faces unprecedented pressures, overcoming polarization and aligning the goals of wilderness defenders and Indigenous peoples is paramount, to avoid environmental degradation.

Pre-colonial Amerindian legacies in forest composition of southern Brazil

Past human societies have left persistent marks on forests worldwide. However, the degree to which pre-colonial Amerindian societies have affected forest structure is still not fully understood, especially in southern Brazil. This study investigated the influence of two distinct Amerindian groups (Southern-Jê and Guarani) over tree composition of forest fragments in the State of Santa Catarina. Vegetation data was obtained from the Santa Catarina Forest and Floristic Inventory (SCFFI): a statewide systematic vegetation sampling project. Archaeological data was collated from literature reviews as well as existing databases for archaeological sites occupied by Guarani and Southern-Jê groups. Using these sites of known Amerindian occupation, and corresponding environmental variables, ecological niche models were developed for each Amerindian group, predicting potential archaeological sites occupied by these groups across southern Brazil. Maps of these potential occupation sites of pre-colonial Amerindian groups were compared with 417 corresponding floristic inventory plots. Redundancy analysis (RDA) was used to identify floristic composition patterns linked to areas with a high probability of Southern-Jê or Guarani presence. Southern-Jê and Guarani pre-colonial occupations overlapped near main rivers; however, Southern-Jê groups generally occupied elevated areas whereas Guarani occupied mostly coastal areas. We observed differences in forest composition associated with the predicted occurrence of these pre-colonial Amerindian groups. Based on these results, we argue there is a relationship between tree species distribution and pre-colonial human occupation by these two Amerindian groups.

A Congo Basin ethnographic analogue of pre-Columbian Amazonian raised fields shows the ephemeral legacy of organic matter management

The functioning and productivity of pre-Columbian raised fields (RFs) and their role in the development of complex societies in Amazonian savannas remain debated. RF agriculture is conducted today in the Congo Basin, offering an instructive analogue to pre-Columbian RFs in Amazonia. Our study of construction of present-day RFs documents periodic addition of organic matter (OM) during repeated field/fallow cycles. Field investigations of RF profiles supported by spectrophotometry reveal a characteristic stratigraphy. Soil geochemistry indicates that the management of Congo RFs improves soil fertility for a limited time when they are under cultivation, but nutrient availability in fallow RFs differs little from that in uncultivated reference topsoils. Furthermore, examination of soil micromorphology shows that within less than 40 years, bioturbation almost completely removes stratigraphic evidence of repeated OM amendments. If Amazonian RFs were similarly managed, their vestiges would thus be unlikely to show traces of such management centuries after abandonment. These results call into question the hypothesis that the sole purpose of constructing RFs in pre-Columbian Amazonia was drainage.

Modifications of the rain forest frugivore community are associated with reduced seed removal at the community level

Tropical rain forests worldwide are under increasing pressure from human activities, which are altering key ecosystem processes such as plant-animal interactions. However, while the direct impact of anthropogenic disturbance on animal communities has been well studied, the consequences of such defaunation for mutualistic interactions such as seed dispersal remains chiefly understood at the plant species level. We asked whether communities of endozoochorous tree species had altered seed removal in forests affected by hunting and logging and if this could be related to modifications of the frugivore community. At two contrasting forest sites in French Guiana, Nouragues (protected) and Montagne de Kaw (hunted and partly logged), we focused on four families of animal-dispersed trees (Sapotaceae, Myristicaceae, Burseraceae, and Fabaceae), which represent 88% of all endozoochorous trees that were fruiting at the time and location of the study. We assessed the abundance of the seed dispersers and predators of these four focal families by conducting diurnal distance sampling along line transects. Densities of several key seed dispersers such as large-bodied primates were greatly reduced at Montagne de Kaw, where the specialist frugivore Ateles paniscus is probably extinct. In parallel, we estimated seed removal rates from fruit and seed counts conducted in 1-m² quadrats placed on the ground beneath fruiting trees. Seed removal rates dropped from 77% at Nouragues to 47 % at Montagne de Kaw, confirming that the loss of frugivores associated with human disturbance impacts seed removal at the community level. In contrast to Sapotaceae, whose seeds are dispersed by mammals only, weaker declines in seed removal for Burseraceae and Myristicaceae suggest that some compensation may occur for these bird- and mammal-dispersed families, possibly because of the high abundance of Toucans at the disturbed site. The defaunation process currently occurring across many tropical forests could dramatically reduce the diversity of entire communities of animal-dispersed trees through seed removal limitation.

Effects of different levels of exploration on the ecological processes of Dimorphandra gardneriana, a tropical savanna tree

The exploitation of forest resources, especially non-timber forest products, has effects on different biological levels, from the biochemical level of an organism to the ecosystem level. The present study addresses the effects of different management strategies (protected area, managed area, and an area where the species is cultivated in agroforestry systems) in reproductive phenology, fruit features, and phytochemical profiles of Dimorphandra gardneriana (Leguminosae), a tree species, pioneer, and socioeconomically important plant of the Brazilian Savanna. Its fruits are exploited by extractivist communities to obtain rutin and quercetin, which are internationally traded bioflavonoids (two of the ten most exported phytochemicals in Brazil). The results showed that the effects on these parameters were characterized as positive, increasing according to the level of exploitation. The agroforestry system had higher yields of flavonoids of economic interest, viable fruits and seeds, followed by the management area and the protected area. Finally, knowledge about the planting effects on fava d'anta fruit production can be a great ally for effectively managing forest resources. A varied system of exploitation implies greater and more stable economic returns for extractive communities, favoring the conservation of the species in protected areas.

Mutualist and pathogen traits interact to affect plant community structure in a spatially explicit model

Empirical studies show that plant-soil feedbacks (PSF) can generate negative density dependent (NDD) recruitment capable of maintaining plant community diversity at landscape scales. However, the observation that common plants often exhibit relatively weaker NDD than rare plants at local scales is difficult to reconcile with the maintenance of overall plant diversity. We develop a spatially explicit simulation model that tracks the community dynamics of microbial mutualists, pathogens, and their plant hosts. We find that net PSF effects vary as a function of both host abundance and key microbial traits (e.g., host affinity) in ways that are compatible with both common plants exhibiting relatively weaker local NDD, while promoting overall species diversity. The model generates a series of testable predictions linking key microbial traits and the relative abundance of host species, to the strength and scale of PSF and overall plant community diversity.

Archaeological expansions in tropical South America during the late Holocene: Assessing the role of demic diffusion

Human expansions motivated by the spread of farming are one of the most important processes that shaped cultural geographies during the Holocene. The best known example of this phenomenon is the Neolithic expansion in Europe, but parallels in other parts of the globe have recently come into focus. Here, we examine the expansion of four archaeological cultures of widespread distribution in lowland South America, most of which originated in or around the Amazon basin and spread during the late Holocene with the practice of tropical forest agriculture. We analyze spatial gradients in radiocarbon dates of each culture through space-time regressions, allowing us to establish the most likely geographical origin, time and speed of expansion. To further assess the feasibility of demic diffusion as the process behind the archaeological expansions in question, we employ agent-based simulations with demographic parameters derived from the ethnography of tropical forest farmers. We find that, while some expansions can be realistically modeled as demographic processes, others are not easily explainable in the same manner, which is possibly due to different processes driving their dispersal (e.g. cultural diffusion) or problematic/incomplete archaeological data.

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.

Platysace (Apiaceae) of south-western Australia: silent story tellers of an ancient human landscape

High gene flow and a population structure corresponding to human rather than geographical drivers are likely to be genetic patterns of human-dispersed plant taxa. We examined variation in geographical structure and gene flow estimates based on three non-coding regions of plastid DNA in three south-west Australian members of the Platysace genus to identify whether a human influence on dispersion of utilized taxa was detectable. Edible tubers of Platysace deflexa and Platysace trachymenioides have been harvested historically by Noongar traditional owners, whereas Platysace effusa has no known cultural significance. We found differences between utilized and non-utilized taxa, particularly when considered against the generally complex phylogeographical patterning in south-west Australian plant taxa. Platysace effusa showed a pattern of high population divergence, low gene flow and multiple refugia, consistent with a long evolutionary history, past climatic oscillations and persistence in a highly fragmented landscape. In contrast, higher gene flow estimates, less divergence between populations and common haplotypes in P. deflexa and in P. trachymenioides over the south-eastern part of its range are consistent with anthropogenic influences. This study contributes to the understanding of human influences on south-west Australian plant taxa that have been present since the late Pleistocene, but to date have received little scientific attention.