Hybridization in palms (Arecaceae)

Hybridization has significant evolutionary consequences across the Tree of Life. The process of hybridization has played a major role in plant evolution and has contributed to species richness and trait variation. Since morphological traits are partially a product of their environment, there may be a link between hybridization and ecology. Plant hybrid species richness is noted to be higher in harsh environments, and we explore this hypothesis with a keystone tropical plant lineage, palms (Arecaceae). Leveraging a recent literature review of naturally occurring palm hybrids, we developed a method to calculate hybrid frequency, and then tested if there is phylogenetic signal of hybrids using a phylogeny of all palms. Further, we used phylogenetic comparative methods to examine the interaction between hybrid frequency and presence in dry environments, on islands, and the species richness of genera. Phylogenetic generalized least squares models had stronger support than models of random association, indicating phylogenetic signal for the presence of hybrids in dry and island environments. However, all p-values were >.05 and therefore the correlation was poor between hybridization and the trait frequencies examined. Presence in particular environments are not strongly correlated to hybrid frequency, but phylogenetic signal suggests a role in its distribution in different habitats. Hybridization in palms is not evenly distributed across subfamilies, tribes, subtribes yet plays an important role in palm diversity, nonetheless. Increasing our understanding hybridization in this economically and culturally important plant family is essential, particularly since rates are projected to increase with climate change, reconfiguring the dynamics and distribution of biodiversity.

Amazon forest biogeography predicts resilience and vulnerability to drought

Amazonia contains the most extensive tropical forests on Earth, but Amazon carbon sinks of atmospheric CO2 are declining, as deforestation and climate-change-associated droughts1-4 threaten to push these forests past a tipping point towards collapse5-8. Forests exhibit complex drought responses, indicating both resilience (photosynthetic greening) and vulnerability (browning and tree mortality), that are difficult to explain by climate variation alone9-17. Here we combine remotely sensed photosynthetic indices with ground-measured tree demography to identify mechanisms underlying drought resilience/vulnerability in different intact forest ecotopes18,19 (defined by water-table depth, soil fertility and texture, and vegetation characteristics). In higher-fertility southern Amazonia, drought response was structured by water-table depth, with resilient greening in shallow-water-table forests (where greater water availability heightened response to excess sunlight), contrasting with vulnerability (browning and excess tree mortality) over deeper water tables. Notably, the resilience of shallow-water-table forest weakened as drought lengthened. By contrast, lower-fertility northern Amazonia, with slower-growing but hardier trees (or, alternatively, tall forests, with deep-rooted water access), supported more-drought-resilient forests independent of water-table depth. This functional biogeography of drought response provides a framework for conservation decisions and improved predictions of heterogeneous forest responses to future climate changes, warning that Amazonia's most productive forests are also at greatest risk, and that longer/more frequent droughts are undermining multiple ecohydrological strategies and capacities for Amazon forest resilience.

Contributions of human cultures to biodiversity and ecosystem conservation

The expansion of globalized industrial societies is causing global warming, ecosystem degradation, and species and language extinctions worldwide. Mainstream conservation efforts still focus on nature protection strategies to revert this crisis, often overlooking the essential roles of Indigenous Peoples and Local Communities (IP&LC) in protecting biodiversity and ecosystems globally. Here we assess the scientific literature to identify relationships between biodiversity (including ecosystem diversity) and cultural diversity, and investigate how these connections may affect conservation outcomes in tropical lowland South America. Our assessment reveals a network of interactions and feedbacks between biodiversity and diverse IP&LC, suggesting interconnectedness and interdependencies from which multiple benefits to nature and societies emerge. We illustrate our findings with five case studies of successful conservation models, described as consolidated or promising 'social-ecological hope spots', that show how engagement with IP&LC of various cultures may be the best hope for biodiversity and ecosystem conservation, particularly when aligned with science and technology. In light of these five inspiring cases, we argue that conservation science and policies need to recognize that protecting and promoting both biological and cultural diversities can provide additional co-benefits and solutions to maintain ecosystems resilient in the face of global changes.

Pre-contact and post-colonial ecological legacies shape Surinamese rainforests

Disturbances in tropical forests can have long-lasting ecological impacts, but their manifestations (ecological legacies) in modern forests are uncertain. Many Amazonian forests bear the mark of past soil modifications, species enrichments, and fire events, but the trajectories of ecological legacies from the pre-contact or post-colonial period remain relatively unexplored. We assessed the fire and vegetation history from 15 soil cores ranging from 0 to 10 km from a post-colonial Surinamese archaeological site. We show that (1) fires occurred from 96 bc to recent times and induced significant vegetation change, (2) persistent ecological legacies from pre-contact and post-colonial fire and deforestation practices were mainly within 1 km of the archaeological site, and (3) palm enrichment of Attalea, Oenocarpus and Astrocaryum occurred within 0, 1, and 8 km of the archaeological site, respectively. Our results challenge the notion of spatially extensive and persistent ecological legacies. Instead, our data indicate that the persistence and extent of ecological legacies are dependent on their timing, frequency, type, and intensity. Examining the mechanisms and manifestations of ecological legacies is crucial in assessing forest resilience and Indigenous and local land rights in the highly threatened Amazonian forests.

Distribution and diversification of Adelphobates, emblematic poison frogs from Brazilian Amazonia

Adelphobates contains three species, and the inaccurate identification of A. quinquevittatus and the scarcity of records of A. castaneoticus complicate inference of their distributions; the latter species occurs in sympatry with A. galactonotus. Our objective was to revise the distributions of Adelphobates by compiling data and modeling habitat suitability, as range limits may be shaped by landscape features and biotic interactions. We initially analyzed the existence of operational taxonomic units within the nominal species and subsequently inferred the observed and potential distributions, taking into account the possible independent lineages for the three species, and we also generated a molecular timetree to understand the chronology of interspecific diversification events. Adelphobates quinquevittatus was found to have a more easterly distribution than previously described, and specimens with phenotypic variation were found to occur in areas inconsistent with the modeling, and A. castaneoticus was concentrated in the Tapajós-Xingu interfluve, surrounded by A. galactonotus. Models indicated that the right bank of the Xingu River is suitable for both species, indeed, both were found there. Despite Adelphobates species having their distributions delimited by major Amazonian rivers, estimated divergence times predate the formation of the modern river network, suggesting that other mechanisms were involved in their diversification.

Advancing ethnobiology for the ecological transition and a more inclusive and just world: a comprehensive framework for the next 20 years

This opinion piece, written by ethnobiologists from different parts of the world, emphasizes the importance of ethnobiology research in advancing contemporary biology, natural resource management, biodiversity conservation, sustainable development, and, especially, contributing to the ecological transition and more just and inclusive world. To achieve these goals, it is essential to develop research and collaborate with social groups that live in close relationship with nature in research activities, such as Indigenous Peoples and Local Communities (IPLC), as well as Afro-descendants and other Marginalized, Minority or Minoritized Communities (AMMC). Ethnobiology can identify and provide locally appropriate solutions to local problems, enabling sustainable resource management at the landscape level. The text explores important aspects that need to be considered to guide the future of ethnobiology in the next 20 years, aiming to integrate and amplify previous discussions held in the discipline and identify points that demand ongoing attention. This paper highlights reflections from diverse researchers, emphasizing how ethnobiology can embrace different perspectives and employ rigorous analysis of complex phenomena toward effective policies and practices. This approach holds the potential to address the challenges the planet is currently facing in the coming decades.

Yams (Dioscorea spp.) in shellmounds and swiddens: ancient history in Babitonga Bay, Santa Catarina State, southern Brazil

BACKGROUND

In Babitonga Bay, southern Brazil, records of yam consumption exist among shellmound builders from at least 4000 years ago. Shellmounds (sambaquis) are anthropogenic structures in the form of mounds with layers of shells associated with other faunal remains, as well as with charcoal, artefacts and burial. Larger sambaquis are considered to be funerary monuments. The indigenous Jê and Guarani people also lived in the region before the European invasion and cultivated yams. Currently, exotic and domesticated yams are cultivated in the region by farmers. Our aim is to describe the long-term history between the people and Dioscorea in the Babitonga Bay region based on its consumption and occurrence in shellmounds and swiddens.

METHODS

Surveys of Dioscorea spp. and host were carried out in the vegetation of shellmounds and in the surrounding area using visual detection through intensive searches in transects using the walking method. The survey of Dioscorea species used and cultivated in the precolonial, colonial and current periods was carried out based on the literature. In the present study, only Dioscorea trifida cultivations were recorded.

RESULTS

Dioscorea cayennensis, Dioscorea chondrocarpa, Dioscorea dodecaneura, Dioscorea laxiflora, Dioscorea olfersiana, and Dioscorea scabra, all recorded in associated vegetation of shellmounds, in different combinations of the species. In swiddens, D. trifida is most common, followed by Dioscorea alata and, to a lesser extent, Dioscorea bulbifera and D. cayennensis. Records of food use prevail, but they are used as medicinal plants. Yams are integrated on anthropogenic soils of shellmounds and in swiddens in monoculture systems or in intercropping with Zea mays or Colocasia esculenta. The presence of exotic food trees and D. cayennensis in some shellmounds indicates the influence of colonizers on the composition of the vegetation. In sambaquis, there are overlapping processes of construction of cultural niches by different human groups at different times.

CONCLUSIONS

The sambaquis and the associated vegetation and swiddens form part of a domesticated landscape. The native species of Dioscorea recorded in shellmounds and surrounding vegetation do not depend on human action to perpetuate themselves in the environment. However, this does not rule out human influence in the past, but it does not indicate horticulture among the Sambaquianos. Greater investment in genetic, archaeobotanical and ethnobotanical research can contribute to a better understanding of the relationship between people and yams over thousands of years.

Anthropogenic disturbance driving population decline of a dominant tree in East Asia evergreen broadleaved forests over the last 11,000 years

Current biodiversity loss is generally considered to have been caused by anthropogenic disturbance, but it is unclear when anthropogenic activities began to affect biodiversity loss. One hypothesis suggests it began with the Industrial Revolution, whereas others propose that anthropogenic disturbance has been associated with biodiversity decline since the early Holocene. To test these hypotheses, we examined the unique vegetation of evergreen broadleaved forests (EBLFs) in East Asia, where humans have affected landscapes since the early Holocene. We adopted a genomic approach to infer the demographic history of a dominant tree (Litsea elongata) of EBLFs. We used Holocene temperature and anthropogenic disturbance factors to calculate the correlation between these variables and the historical effective population size of L. elongata with Spearman statistics and integrated the maximum-entropy niche model to determine the impact of climate change and anthropogenic disturbance on fluctuation in its effective population size. We identified 9 well-defined geographic clades for the populations of L. elongata. Based on the estimated historical population sizes of these clades, all the populations contracted, indicating persistent population decline over the last 11,000 years. Demographic history of L. elongata and human population change, change in cropland use, and change in irrigated rice area were significantly negatively correlated, whereas climate change in the Holocene was not correlated with demographic history. Our results support the early human impact hypothesis and provide comprehensive evidence that early anthropogenic disturbance may contribute to the current biodiversity crisis in East Asia.

Towards richer knowledge partnerships between ecology and ethnoecology

Indigenous and traditional practices based on ethnoecological knowledge are fundamental to biodiversity stewardship and sustainable use. Knowledge partnerships between Indigenous Peoples, traditional local communities, and ecologists can produce richer and fairer understandings of nature. We identify key topical areas where such collaborations can positively transform science, policy, and practice.

Critical transitions in the Amazon forest system

The possibility that the Amazon forest system could soon reach a tipping point, inducing large-scale collapse, has raised global concern1-3. For 65 million years, Amazonian forests remained relatively resilient to climatic variability. Now, the region is increasingly exposed to unprecedented stress from warming temperatures, extreme droughts, deforestation and fires, even in central and remote parts of the system1. Long existing feedbacks between the forest and environmental conditions are being replaced by novel feedbacks that modify ecosystem resilience, increasing the risk of critical transition. Here we analyse existing evidence for five major drivers of water stress on Amazonian forests, as well as potential critical thresholds of those drivers that, if crossed, could trigger local, regional or even biome-wide forest collapse. By combining spatial information on various disturbances, we estimate that by 2050, 10% to 47% of Amazonian forests will be exposed to compounding disturbances that may trigger unexpected ecosystem transitions and potentially exacerbate regional climate change. Using examples of disturbed forests across the Amazon, we identify the three most plausible ecosystem trajectories, involving different feedbacks and environmental conditions. We discuss how the inherent complexity of the Amazon adds uncertainty about future dynamics, but also reveals opportunities for action. Keeping the Amazon forest resilient in the Anthropocene will depend on a combination of local efforts to end deforestation and degradation and to expand restoration, with global efforts to stop greenhouse gas emissions.

Consistent patterns of common species across tropical tree communities

Trees structure the Earth's most biodiverse ecosystem, tropical forests. The vast number of tree species presents a formidable challenge to understanding these forests, including their response to environmental change, as very little is known about most tropical tree species. A focus on the common species may circumvent this challenge. Here we investigate abundance patterns of common tree species using inventory data on 1,003,805 trees with trunk diameters of at least 10 cm across 1,568 locations1-6 in closed-canopy, structurally intact old-growth tropical forests in Africa, Amazonia and Southeast Asia. We estimate that 2.2%, 2.2% and 2.3% of species comprise 50% of the tropical trees in these regions, respectively. Extrapolating across all closed-canopy tropical forests, we estimate that just 1,053 species comprise half of Earth's 800 billion tropical trees with trunk diameters of at least 10 cm. Despite differing biogeographic, climatic and anthropogenic histories7, we find notably consistent patterns of common species and species abundance distributions across the continents. This suggests that fundamental mechanisms of tree community assembly may apply to all tropical forests. Resampling analyses show that the most common species are likely to belong to a manageable list of known species, enabling targeted efforts to understand their ecology. Although they do not detract from the importance of rare species, our results open new opportunities to understand the world's most diverse forests, including modelling their response to environmental change, by focusing on the common species that constitute the majority of their trees.

Indigenous Peoples' Lands are critical for safeguarding vertebrate diversity across the tropics

Indigenous Peoples are long-term custodians of their lands, but only recently are their contributions to conservation starting to be recognized in biodiversity policy and practice. Tropical forest loss and degradation are lower in Indigenous lands than unprotected areas, yet the role of Indigenous Peoples' Lands (IPL) in biodiversity conservation has not been properly assessed from regional to global scales. Using species distribution ranges of 11,872 tropical forest-dependent vertebrates to create area of habitat maps, we identified the overlap of these species ranges with IPL and then compared values inside and outside of IPL for species richness, extinction vulnerability, and range-size rarity. Of assessed vertebrates, at least 76.8% had range overlaps with IPL, on average overlapping ~25% of their ranges; at least 120 species were found only within IPL. Species richness within IPL was highest in South America, while IPL in Southeast Asia had highest extinction vulnerability, and IPL in Dominica and New Caledonia were important for range-size rarity. Most countries in the Americas had higher species richness within IPL than outside, whereas most countries in Asia had lower extinction vulnerability scores inside IPL and more countries in Africa and Asia had slightly higher range-size rarity in IPL. Our findings suggest that IPL provide critical support for tropical forest-dependent vertebrates, highlighting the need for greater inclusion of Indigenous Peoples in conservation target-setting and program implementation, and stronger upholding of Indigenous Peoples' rights in conservation policy.

Mapping density, diversity and species-richness of the Amazon tree flora

Using 2.046 botanically-inventoried tree plots across the largest tropical forest on Earth, we mapped tree species-diversity and tree species-richness at 0.1-degree resolution, and investigated drivers for diversity and richness. Using only location, stratified by forest type, as predictor, our spatial model, to the best of our knowledge, provides the most accurate map of tree diversity in Amazonia to date, explaining approximately 70% of the tree diversity and species-richness. Large soil-forest combinations determine a significant percentage of the variation in tree species-richness and tree alpha-diversity in Amazonian forest-plots. We suggest that the size and fragmentation of these systems drive their large-scale diversity patterns and hence local diversity. A model not using location but cumulative water deficit, tree density, and temperature seasonality explains 47% of the tree species-richness in the terra-firme forest in Amazonia. Over large areas across Amazonia, residuals of this relationship are small and poorly spatially structured, suggesting that much of the residual variation may be local. The Guyana Shield area has consistently negative residuals, showing that this area has lower tree species-richness than expected by our models. We provide extensive plot meta-data, including tree density, tree alpha-diversity and tree species-richness results and gridded maps at 0.1-degree resolution.

Sensing Forests Directly: The Power of Permanent Plots

The need to measure, monitor, and understand our living planet is greater than ever. Yet, while many technologies are applied to tackle this need, one developed in the 19th century is transforming tropical ecology. Permanent plots, in which forests are directly sensed tree-by-tree and species-by-species, already provide a global public good. They could make greater contributions still by unlocking our potential to understand future ecological change, as the more that computational and remote technologies are deployed the greater the need to ground them with direct observations and the physical, nature-based skills of those who make them. To achieve this requires building profound connections with forests and disadvantaged communities and sustaining these over time. Many of the greatest needs and opportunities in tropical forest science are therefore not to be found in space or in silico, but in vivo, with the people, places and plots who experience nature directly. These are fundamental to understanding the health, predicting the future, and exploring the potential of Earth's richest ecosystems. Now is the time to invest in the tropical field research communities who make so much possible.

Long-term Ecological Research: Chasing fashions or being prepared for fashion changes?

Long-term-ecological-research (LTER) faces many challenges, including the difficulty of obtaining long-term funding, changes in research questions and sampling designs, keeping researchers collecting standardized data for many years, impediments to interactions with local people, and the difficulty of integrating the needs of local decision makers with "big science". These issues result in a lack of universally accepted guidelines as to how research should be done and integrated among LTER sites. Here we discuss how the RAPELD (standardized field infrastructure system), can help deal with these issues as a complementary technique in LTER studies, allowing comparisons across landscapes and ecosystems and reducing sampling costs. RAPELD uses local surveys to understand broad spatial and temporal patterns while enhancing decision-making and training of researchers, local indigenous groups and traditional communities. Sampling of ecological data can be carried out by different researchers through standardized protocols, resulting in spatial data that can be used to answer temporal questions, and allow new questions to be investigated. Results can also be integrated into existing biodiversity networks. Integrated systems are the most efficient way to save resources, maximize results, and accumulate information that can be used in the face of the unknown unknowns upon which our future depends.

More than 10,000 pre-Columbian earthworks are still hidden throughout Amazonia

Indigenous societies are known to have occupied the Amazon basin for more than 12,000 years, but the scale of their influence on Amazonian forests remains uncertain. We report the discovery, using LIDAR (light detection and ranging) information from across the basin, of 24 previously undetected pre-Columbian earthworks beneath the forest canopy. Modeled distribution and abundance of large-scale archaeological sites across Amazonia suggest that between 10,272 and 23,648 sites remain to be discovered and that most will be found in the southwest. We also identified 53 domesticated tree species significantly associated with earthwork occurrence probability, likely suggesting past management practices. Closed-canopy forests across Amazonia are likely to contain thousands of undiscovered archaeological sites around which pre-Columbian societies actively modified forests, a discovery that opens opportunities for better understanding the magnitude of ancient human influence on Amazonia and its current state.

Intentional creation of carbon-rich dark earth soils in the Amazon

Fertile soil known as Amazonian dark earth is central to the debate over the size and ecological impact of ancient human populations in the Amazon. Dark earth is typically associated with human occupation, but it is uncertain whether it was created intentionally. Dark earth may also be a substantial carbon sink, but its spatial extent and carbon inventory are unknown. We demonstrate spatial and compositional similarities between ancient and modern dark earth and document modern Indigenous practices that enrich soil, which we use to propose a model for the formation of ancient dark earth. This comparison suggests that ancient Amazonians managed soil to improve fertility and increase crop productivity. These practices also sequestered and stored carbon in the soil for centuries, and we show that some ancient sites contain as much carbon as the above-ground rainforest biomass. Our results demonstrate the intentional creation of dark earth and highlight the value of Indigenous knowledge for sustainable rainforest management.

Forest disturbance and recovery in Peruvian Amazonia

Amazonian forests function as biomass and biodiversity reservoirs, contributing to climate change mitigation. While they continuously experience disturbance, the effect that disturbances have on biomass and biodiversity over time has not yet been assessed at a large scale. Here, we evaluate the degree of recent forest disturbance in Peruvian Amazonia and the effects that disturbance, environmental conditions and human use have on biomass and biodiversity in disturbed forests. We integrate tree-level data on aboveground biomass (AGB) and species richness from 1840 forest plots from Peru's National Forest Inventory with remotely sensed monitoring of forest change dynamics, based on disturbances detected from Landsat-derived Normalized Difference Moisture Index time series. Our results show a clear negative effect of disturbance intensity tree species richness. This effect was also observed on AGB and species richness recovery values towards undisturbed levels, as well as on the recovery of species composition towards undisturbed levels. Time since disturbance had a larger effect on AGB than on species richness. While time since disturbance has a positive effect on AGB, unexpectedly we found a small negative effect of time since disturbance on species richness. We estimate that roughly 15% of Peruvian Amazonian forests have experienced disturbance at least once since 1984, and that, following disturbance, have been increasing in AGB at a rate of 4.7 Mg ha-1  year-1 during the first 20 years. Furthermore, the positive effect of surrounding forest cover was evident for both AGB and its recovery towards undisturbed levels, as well as for species richness. There was a negative effect of forest accessibility on the recovery of species composition towards undisturbed levels. Moving forward, we recommend that forest-based climate change mitigation endeavours consider forest disturbance through the integration of forest inventory data with remote sensing methods.

New patterns of the tree beta diversity and its determinants in the largest savanna and wetland biomes of South America

Clear and data-driven bioregionalizations can provide a framework to test hypotheses and base biodiversity conservation. Here we used occurrence and abundance data in combination with objective analytical methods to propose two bioregionalization schemes for tree species of the Cerrado and the Pantanal in South America. We also evaluated the contribution of three sets of determinants of the occurrence- and abundance-based subregions. We compiled data on tree species composition from 894 local assemblages based on species occurrences, and from 658 local assemblages based on species abundances. We used an unconstrained community-level modelling approach and clustering techniques to identify and map tree subregions for the occurrence and the abundance data sets, separately. Hierarchical clustering analyses were conducted to investigate floristic affinities between the subregions and to map broader floristic regions. We used multinomial logistic regression models, deviance partitioning, and rank-sum tests to assess the main subregion correlates. We identified 18 occurrence- and four abundance-based subregions in the Cerrado-Pantanal. The hierarchical classifications grouped the occurrence-based subregions into nine floristic zones and abundance-based subregions into two broad floristic zones. Variation in subregions were explained mainly by environmental factors and spatial structure in both occurrence and abundance data sets. The occurrence- and abundance-based subregions are complementary approaches to disentangle macroecological patterns and to plan conservation efforts in the Cerrado and the Pantanal. Our findings based on occurrence data revealed more complex and interdigitated boundaries between subregions of tree species than previously reported. The environment, historical stability, and human effects act in a synergetic way on the distribution of the subregions. Finally, the relevance of contemporary environmental factors to the subregion patterns we found alert us to the profound impact global warming may have on the spatial organization of the Cerrado-Pantanal tree flora.

Phytolith assemblages reflect variability in human land use and the modern environment

Phytoliths preserved in soils and sediments can be used to provide unique insights into past vegetation dynamics in response to human and climate change. Phytoliths can reconstruct local vegetation in terrestrial soils where pollen grains typically decay, providing a range of markers (or lack thereof) that document past human activities. The ca. 6 million km2 of Amazonian forests have relatively few baseline datasets documenting changes in phytolith representation across gradients of human disturbances. Here we show that phytolith assemblages vary on local scales across a gradient of (modern) human disturbance in tropical rainforests of Suriname. Detrended correspondence analysis showed that the phytolith assemblages found in managed landscapes (shifting cultivation and a garden), unmanaged forests, and abandoned reforesting sites were clearly distinguishable from intact forests and from each other. Our results highlight the sensitivity and potential of phytoliths to be used in reconstructing successional trajectories after site usage and abandonment. Percentages of specific phytolith morphotypes were also positively correlated with local palm abundances derived from UAV data, and with biomass estimated from MODIS satellite imagery. This baseline dataset provides an index of likely changes that can be observed at other sites that indicate past human activities and long-term forest recovery in Amazonia.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00334-023-00932-2.

Prehistoric pathways to Anthropocene adaptation: Evidence from the Red River Delta, Vietnam

Over the past twenty years, government advisory bodies have placed increasing emphasis on the need for adaptive measures in response to the effects of human-induced climate change. Integrated Assessment Models (IAMs), which incorporate macroeconomic and climate variables, feature prominently in advisory content, though they rarely draw on data from outside strictly constrained hypothetical systems. This has led to assertions that they are not well-suited to approximate complex systemic human-environment processes. Modular, interdisciplinary approaches have offered a way to address this shortcoming; however, beyond climate records, prehistoric data continue to be under-utilised in developing such models. In this paper we highlight the contribution that archaeology and palaeoecology can make to the development of the next generation IAMs that are expected to enhance provision for more local and pro-active adaptations to future climate change. We present data from one of Southeast Asia's most heavily developed river deltas: the Red River (Song Hong) Delta, in Vietnam and localised analysis from the Tràng An Landscape Complex World Heritage Site, on the delta's southern margin. Comparison is made between Shared Socio-economic Pathways (SSP) 5-8.5 and SSP2-4.5 emission projection models and the Mid-Holocene inundation of the Red River Basin. We highlight the value to taking a scientific long view of coastal evolution through an illustrative set of eight research foci where palaeo-data can bring new and localised empirical data to bear on future risk management planning. We proceed to demonstrate the applicability of palaeoenvironmental, zooarchaeological and historical evidence to management and the development of sustainable conservation strategies using Tràng An as a case study. In so doing, we further highlight the importance of knowledge exchange between scientific, corporate, non-governmental, local, and state stakeholders to achieve tangible results on the ground.

Relationship between fruit phenotypes and domestication in hexaploid populations of biribá (Annona mucosa) in Brazilian Amazonia

Background

Biribá (Annona mucosa Jacq.) is a fruit tree domesticated in Amazonia and has polyploid populations. The species presents ample phenotypic variation in fruit characteristics, including weight (100-4,000 g) and differences in carpel protrusions. Two cytotypes are recorded in the literature (2n = 28, 42) and genome size records are divergent (2C = 4.77, 5.42 and 6.00 pg). To decipher the role of polyploidy in the domestication of A. mucosa, we examined the relationships among phenotypic variation, chromosome number and genome size, and which came first, polyploidization or domestication.

Methodology

We performed chromosome counts of A. mucosa from central and western Brazilian Amazonia, and estimated genome size by flow cytometry. We performed phylogenetic reconstruction with publicly available data using a Bayesian framework, time divergence analysis and reconstructed the ancestral chromosome number for the genus Annona and for A. mucosa.

Results

We observed that variation in fruit phenotypes is not associated with variation in chromosome number and genome size. The most recent common ancestor of A. mucosa is inferred to be polyploid and diverged before domestication.

Conclusions

We conclude that, when domesticated, A. mucosa was already polyploid and we suggest that human selection is the main evolutionary force behind fruit size and fruit morphological variation in Annona mucosa.

Local working collections as the foundation for an integrated conservation of Theobroma cacao L. in Latin America

The intraspecific diversity of cacao has traditionally been preserved in genebanks. However, these establishments face various challenges, notably insufficient funding, accession redundancy, misidentification and lack of wild cacao population samples. In natural environments, it is expected that unknown varieties of cacao may still be found, but wild populations of cacao are increasingly threatened by climate change, deforestation, habitat loss, land use changes and poor knowledge. Farmers also retain diversity, but on-farm conservation is affected by geopolitical, economic, management and cultural issues, that are influenced at multiple scales, from the household to the international market. Taking separately, ex situ, in situ and on-farm conservation have not achieved adequate conservation fostering the inclusion of all stakeholders and the broad use of cacao diversity. We analyze the use of the traditional conservation strategies (ex situ, in situ and on-farm) and propose an integrated approach based on local working collections to secure cacao diversity in the long term. We argue that national conservation networks should be implemented in countries of origin to simultaneously maximize alpha (diversity held in any given working collection), beta (the change in diversity between working collections in different regions) and gamma diversity (overall diversity in a country).

Bearing Fruit: Miocene Apes and Rosaceous Fruit Evolution

Extinct megafaunal mammals in the Americas are often linked to seed-dispersal mutualisms with large-fruiting tree species, but large-fruiting species in Europe and Asia have received far less attention. Several species of arboreal Maloideae (apples and pears) and Prunoideae (plums and peaches) evolved large fruits starting around nine million years ago, primarily in Eurasia. As evolutionary adaptations for seed dispersal by animals, the size, high sugar content, and bright colorful visual displays of ripeness suggest that mutualism with megafaunal mammals facilitated the evolutionary change. There has been little discussion as to which animals were likely candidate(s) on the late Miocene landscape of Eurasia. We argue that several possible dispersers could have consumed the large fruits, with endozoochoric dispersal usually relying on guilds of species. During the Pleistocene and Holocene, the dispersal guild likely included ursids, equids, and elephantids. During the late Miocene, large primates were likely also among the members of this guild, and the potential of a long-held mutualism between the ape and apple clades merits further discussion. If primates were a driving factor in the evolution of this large-fruit seed-dispersal system, it would represent an example of seed-dispersal-based mutualism with hominids millions of years prior to crop domestication or the development of cultural practices, such as farming.

Amazonian Invertebrates in the Traditional diet of the Paiter Suruí in Southeastern Brazil

The Paiter Suruí people in the southwestern Brazilian Amazon have a complex food system that includes insects and crustaceans. We designed our study to systematize data about the invertebrates they incorporate into their traditional diet. After conducting a review of the literature, we verified and expanded the data through semi-structured interviews with Paiter Suruí volunteers, and traced trends in their consumption of invertebrates. We identified 61 invertebrates, including 58 insects of the orders Coleoptera, Lepidoptera, Hymenoptera, and three crustaceans. While beetle larvae remain a popular choice, consumption of other insects and crustaceans seems to have diminished over time.

Spatial structure of the Caatinga woody flora: abundance patterns have environmental, Pleistocene, and indigenous drivers

Despite growing knowledge on the distribution and functioning of dryland vegetation types, their internal biodiversity structure (i.e., subregions) is much less studied. In the delineation of subregions, the use of species occurrence or abundance data may reveal different aspects of metacommunity structure. We revisit the issue of the bioregionalization of the woody flora of the Caatinga, the largest block of the dry forest and woodland biome in Latin America, using abundance data. We also evaluated the drivers of the spatial distribution of plant subregions: historical, current environmental and human effects. Using a K-means partition on interpolated NMDS axes, we identified 10 abundance subregions. Aridity, topography and soil, biome stability since the Pleistocene, and historical indigenous effects were retained by a Multinomial Logistic regression model, and their combined fractions explained most of the abundance variability in subregions. The subregions we present may support spatialized conservation and management decisions in the lack of detailed local data. The present results confirm the Caatinga woody flora broad composition patterns uncovered using presence-absence data in previous studies. Additionally, we found larger subregions than those identified with presence and absence data, suggesting the existence of oligarchies of dominant species in distinct parts of the Caatinga biome.

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.

Scrutinizing the paleoecological record of the Maya forest

Human expansion into and occupation of the New World coincided with the great transition from the Pleistocene to the Holocene epoch, yet questions remain about how we detect human presence in the paleoecological record. In the Maya area of southern Mesoamerica, archeological evidence of the human imprint is largely invisible until ∼4,000 years ago. How do environmental changes after that time correspond and relate to human impacts? Are the archeological signatures of initial settlements in the Early Preclassic detected? Later, by ∼2,000 years ago when the Maya had fully settled the landscape, how does the evidence of forest compositional changes relate to human intervention? This paper evaluates published paleoecological data in light of the rise of the Maya civilization and reflects on interpretations of how swidden agriculture and the milpa cycle impacted the environment. Evaluating the contrast between the long archeological sequence of successful Maya development and paleoecological interpretations of destructive human-induced environmental impacts requires a concordance among pollen data, archeological evidence, ethnohistoric observations, ethnological studies of traditional Maya land use, and the historical ecology of the Maya forest today.

Indigenous lands in protected areas have high forest integrity across the tropics

Intact tropical forests have a high conservation value.¹ Although perceived as wild,² they have been under long-term human influence.³ As global area-based conservation targets increase, the ecological contributions of Indigenous peoples through their governance institutions and practices⁴ are gaining mainstream interest. Indigenous lands-covering a quarter of Earth's surface⁵ and overlapping with a third of intact forests⁶-often have reduced deforestation, degradation, and carbon emissions, compared with non-protected areas and protected areas.^7,8 A key question with implications for the design of more equitable and effective conservation policies is to understand the impacts of Indigenous lands on forest integrity and long-term use, as critical measures of ecosystem health included within the post-2020 Global Biodiversity Framework.⁹ Using the forest landscape integrity index¹⁰ and Anthromes¹¹ datasets, we find that high-integrity forests tend to be located within the overlap of protected areas and Indigenous lands (protected-Indigenous areas). After accounting for location biases through statistical matching and regression, protected-Indigenous areas had the highest protective effect on forest integrity and the lowest land-use intensity relative to Indigenous lands, protected areas, and non-protected controls pan-tropically. The protective effect of Indigenous lands on forest integrity was lower in Indigenous lands than in protected areas and non-protected areas in the Americas and Asia. The combined positive effects of state legislation and Indigenous presence in protected-Indigenous areas may contribute to maintaining tropical forest integrity. Understanding management and governance in protected-Indigenous areas can help states to appropriately support community-governed lands.

Incorporating a palaeo-perspective into Andean montane forest restoration

Reference ecosystems used in tropical forest restoration lack the temporal dimension required to characterise a mature or intact vegetation community. Here we provide a practical ‘palaeo-reference ecosystem’ for the eastern Andean forests of Ecuador to complement the standard ‘reference ecosystem’ approach. Pollen assemblages from sedimentary archives recovered from Ecuadorian montane forests are binned into distinct time periods and characterised as 1) Ancient (pre-human arrival), 2) Pre-European (Indigenous cultivation), 3) Successional (European arrival/Indigenous depopulation), 4) Mature (diminished human population), 5) Deforested (re-colonisation), and 6) Modern (industrial agriculture). A multivariate statistical approach is then used to identify the most recent period in which vegetation can be characterised as mature. Detrended correspondence analysis indicates that the pollen spectra from CE 1718-1819 (time bin 4 – Mature (diminished human population)) is most similar to that of a pre-human arrival mature or intact state. The pollen spectra of this period are characterised by Melastomataceae, Fabaceae, Solanaceae and Weinmannia. The vegetation of the 1700s, therefore, provides the most recent phase of substantial mature vegetation that has undergone over a century of recovery, representing a practical palaeo-reference ecosystem. We propose incorporating palynological analyses of short cores spanning the last 500 years with botanical inventory data to achieve more realistic and long-term restoration goals.

Feedback in tropical forests of the Anthropocene

Tropical forests are complex systems containing myriad interactions and feedbacks with their biotic and abiotic environments, but as the world changes fast, the future of these ecosystems becomes increasingly uncertain. In particular, global stressors may unbalance the feedbacks that stabilize tropical forests, allowing other feedbacks to propel undesired changes in the whole ecosystem. Here, we review the scientific literature across various fields, compiling known interactions of tropical forests with their environment, including the global climate, rainfall, aerosols, fire, soils, fauna, and human activities. We identify 170 individual interactions among 32 elements that we present as a global tropical forest network, including countless feedback loops that may emerge from different combinations of interactions. We illustrate our findings with three cases involving urgent sustainability issues: (1) wildfires in wetlands of South America; (2) forest encroachment in African savanna landscapes; and (3) synergistic threats to the peatland forests of Borneo. Our findings reveal an unexplored world of feedbacks that shape the dynamics of tropical forests. The interactions and feedbacks identified here can guide future qualitative and quantitative research on the complexities of tropical forests, allowing societies to manage the nonlinear responses of these ecosystems in the Anthropocene.

Late Holocene dietary and cultural variability on the Xingu River, Amazon Basin: A stable isotopic approach

Although once considered a 'counterfeit paradise', the Amazon Basin is now a region of increasing interest in discussions of pre-colonial tropical land-use and social complexity. Archaeobotany, archaeozoology, remote sensing and palaeoecology have revealed that, by the Late Holocene, populations in different parts of the Amazon Basin were using various domesticated plants, modifying soils, building earthworks, and even forming 'Garden Cities' along the Amazon River and its tributaries. However, there remains a relatively limited understanding as to how diets, environmental management, and social structures varied across this vast area. Here, we apply stable isotope analysis to human remains (n = 4 for collagen, n = 17 for tooth enamel), and associated fauna (n = 61 for collagen, n = 28 for tooth enamel), to directly determine the diets of populations living in the Volta Grande do Rio Xingu, an important region of pre-Columbian cultural interactions, between 390 cal. years BC and 1,675 cal. years AD. Our results highlight an ongoing dietary focus on C3 plants and wild terrestrial fauna and aquatic resources across sites and time periods, with varying integration of C4 plants (i.e. maize). We argue that, when compared to other datasets now available from elsewhere in the Amazon Basin, our study highlights the development of regional adaptations to local watercourses and forest types.

Wilderness forms and their implications for global environmental policy and conservation

With the intention of securing industry-free land and seascapes, protecting wilderness entered international policy as a formal target for the first time in the zero draft of the Post-2020 Global Biodiversity Framework under the Convention on Biological Diversity. Given this increased prominence in international policy, it is timely to consider the extent to which the construct of wilderness supports global conservation objectives. We evaluated the construct by overlaying recently updated cumulative human pressure maps that offer a global-scale delineation of industry-free land as wilderness with maps of carbon stock, species richness, and ground travel time from urban centers. Wilderness areas took variable forms in relation to carbon stock, species richness, and proximity to urban centers, where 10% of wilderness areas represented high carbon and species richness, 20% low carbon and species richness, and 3% high levels of remoteness (>48 h), carbon, and species richness. Approximately 35% of all remaining wilderness in 2013 was accessible in <24 h of travel time from urban centers. Although the construct of wilderness can be used to secure benefits in specific contexts, its application in conservation must account for contextual and social implications. The diverse characterization of wilderness under a global environmental conservation lens shows that a nuanced framing and application of the construct is needed to improve understanding, communication, and retention of its variable forms as industry-free places.

Strong floristic distinctiveness across Neotropical successional forests

Forests that regrow naturally on abandoned fields are important for restoring biodiversity and ecosystem services, but can they also preserve the distinct regional tree floras? Using the floristic composition of 1215 early successional forests (≤20 years) in 75 human-modified landscapes across the Neotropic realm, we identified 14 distinct floristic groups, with a between-group dissimilarity of 0.97. Floristic groups were associated with location, bioregions, soil pH, temperature seasonality, and water availability. Hence, there is large continental-scale variation in the species composition of early successional forests, which is mainly associated with biogeographic and environmental factors but not with human disturbance indicators. This floristic distinctiveness is partially driven by regionally restricted species belonging to widespread genera. Early secondary forests contribute therefore to restoring and conserving the distinctiveness of bioregions across the Neotropical realm, and forest restoration initiatives should use local species to assure that these distinct floras are maintained.

Anthropogenic legacies shaping the present composition of demarcation trees in a temperate upland field landscape in Japan

BACKGROUND

Isolated trees are often planted in agricultural landscapes around the world, but their planting background often remains unclear. In this study, we examined the history of demarcation trees in Ibaraki Prefecture in eastern Japan by using land dispute records mainly from the early modern period (from 1600 to 1868), the Rapid Survey Map (RSM) drawn in the late nineteenth century, demarcation tree records from 2011, and interviews of the local residents.

METHODS

We reviewed 39 documents on land disputes to examine the temporal and spatial usage of demarcation tree species in the early modern period. The association between the present distribution of 1486 individuals of six demarcation tree species and past land use in the RSM were analyzed with Fisher's exact test and residual analysis. In addition, we conducted interviews with 48 farmers, most of whom were over 60 years old.

RESULTS

The demarcation plants in vast communal lands and village boundaries in the early modern period were mostly visually prominent tall trees, usually pines. In contrast, smaller trees were planted for demarcation in small-scale areas of forests and farmlands. Although Pourthiaea villosa (Thunb.) DC. Has been planted since the mid-eighteenth century, its planting seems to have accelerated as communal forests were divided mainly in the Meiji period (from 1868 to 1912). The present dominant state of Deutzia crenata Siebold et Zucc. in older farmlands and its ritual use, history of upland field development in the Kanto region, and ancient demarcation use in central Japan indicate its original use may date back to the medieval (from 1185 to 1600) or ancient ritsuryo period (from the seventh century to 1185). Tea (Camellia sinensis (L.) Kuntze) and mulberry (Morus spp.) individuals were considered as early modern or modern crop remnants. Results from the map-based analysis and interviews clarified the recent increase in the use of Euonymus japonicus Thunb. and Celtis sinensis Pers. for demarcation.

CONCLUSIONS

Chronologically dynamic anthropogenic legacies have shaped the present agricultural landscape with different demarcation tree species. A better understanding of the dynamic transformation of vegetation under human influence adds to the historical heritage value of the landscape and should motivate its conservation.

Forests and Farmers: GIS Analysis of Forest Islands and Large Raised Fields in the Bolivian Amazon

The Llanos de Mojos of the Bolivian Amazon is a domesticated landscape with a long history of management by pre-Columbian communities. This paper uses a landscape approach to interpret the settlement patterns of pre-Columbian raised-field farmers in west central Mojos. The pre-Columbian landscape was reconstructed by mapping the distribution of three types of landscape features: forest islands, raised agricultural fields, and water systems (rivers, streams and wetlands). Previous research has identified four types of patterned clustering or ‘constellations’ of these landscape features in west central Mojos. These constellations and the immediate area of the landscape that surrounds them afforded Mojos farmers a specific set of tasks or activities to take part in as part of harnessing resources from the landscape. The mapping of landscape features and their associated tasks onto the landscape provides insight into the organization of the communities that constructed and managed them. It was found that the landscape of west central Mojos is organized into two distinct regional patterns. In the northern part of the region, evidence of large farming communities is dispersed along the banks of the permanent rivers with networks of landscape features extending off into remote areas of the savanna. In the southern part of the region, evidence for large farming communities is clustered closer together in remote areas of the savanna with networks of landscape features extending back towards the permanent rivers. The two regions are melded together by a transitional zone that implies a type of interaction between the regions rather than a distinct separation.

N,N-dimethyltryptamine and Amazonian ayahuasca plant medicine

OBJECTIVE

Reports have indicated possible uses of ayahuasca for the treatment of conditions including depression, addictions, post-traumatic stress disorder, anxiety and specific psychoneuroendocrine immune system pathologies. The article assesses potential ayahuasca and N,N-dimethyltryptamine (DMT) integration with contemporary healthcare. The review also seeks to provide a summary of selected literature regarding the mechanisms of action of DMT and ayahuasca; and assess to what extent the state of research can explain reports of unusual phenomenology.

DESIGN

A narrative review.

RESULTS

Compounds in ayahuasca have been found to bind to serotonergic receptors, glutaminergic receptors, sigma-1 receptors, trace amine-associated receptors, and modulate BDNF expression and the dopaminergic system. Subjective effects are associated with increased delta and theta oscillations in amygdala and hippocampal regions, decreased alpha wave activity in the default mode network, and stimulations of vision-related brain regions particularly in the visual association cortex. Both biological processes and field of consciousness models have been proposed to explain subjective effects of DMT and ayahuasca, however, the evidence supporting the proposed models is not sufficient to make confident conclusions. Ayahuasca plant medicine and DMT represent potentially novel treatment modalities.

CONCLUSIONS

Further research is required to clarify the mechanisms of action and develop treatments which can be made available to the general public. Integration between healthcare research institutions and reputable practitioners in the Amazon is recommended.

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'.

A palaeoecological perspective on the transformation of the tropical Andes by early human activity

Palaeoecological records suggest that humans have been in the Andes since at least 14 000 years ago. Early human impacts on Andean ecosystems included an increase in fire activity and the extinction of the Pleistocene megafauna. These changes in Andean ecosystems coincided with rapid climate change as species were migrating upslope in response to deglacial warming. Microrefugia probably played a vital role in the speed and genetic composition of that migration. The period from ca 14 500 to 12 500 years ago was when novel combinations of plant species appeared to form no-analogue assemblages in the Andes. By 12 000 years ago most areas in what are today the Andean grasslands were being burned and modified by human activity. As the vegetation of these highland settings has been modified by human activity for the entirety of the Holocene, they should be regarded as long-term manufactutred landscapes. The sharp tree lines separating Andean forests from grasslands that we see today were probably also created by repeated burning and owe their position more to human-induced fire than climatic constraints. In areas that were readly penetrated by humans on the forested slopes of the Andes, substantial modification and settlement had occurred by the mid-Holocene. In hard-to-reach areas, however, the amount of human modification may always have been minimal, and these slopes can be considered as being close to natural in their vegetation. 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'.

Legacies of Indigenous land use and cultural burning in the Bolivian Amazon rainforest ecotone

The southwestern Amazon Rainforest Ecotone (ARE) is the transitional landscape between the tropical forest and seasonally flooded savannahs of the Bolivian Llanos de Moxos. These heterogeneous landscapes harbour high levels of biodiversity and some of the earliest records of human occupation and plant domestication in Amazonia. While persistent Indigenous legacies have been demonstrated elsewhere in the Amazon, it is unclear how past human-environment interactions may have shaped vegetation composition and structure in the ARE. Here, we examine 6000 years of archaeological and palaeoecological data from Laguna Versalles (LV), Bolivia. LV was dominated by stable rainforest vegetation throughout the Holocene. Maize cultivation and cultural burning are present after ca 5700 cal yr BP. Polyculture cultivation of maize, manioc and leren after ca 3400 cal yr BP predates the formation of Amazonian Dark/Brown Earth (ADE/ABE) soils (approx. 2400 cal yr BP). ADE/ABE formation is associated with agroforestry indicated by increased edible palms, including Mauritia flexuosa and Attalea sp., and record levels of burning, suggesting that fire played an important role in agroforestry practices. The frequent use of fire altered ADE/ABD forest composition and structure by controlling ignitions, decreasing fuel loads and increasing the abundance of plants preferred by humans. Cultural burning and polyculture agroforestry provided a stable subsistence strategy that persisted despite pronounced climate change and cultural transformations and has an enduring legacy in ADE/ABE forests in the ARE. This article is part of the theme issue 'Tropical forests in the deep human past'.

Genomic Screening to Identify Food Trees Potentially Dispersed by Precolonial Indigenous Peoples

Over millennia, Indigenous peoples have dispersed the propagules of non-crop plants through trade, seasonal migration or attending ceremonies; and potentially increased the geographic range or abundance of many food species around the world. Genomic data can be used to reconstruct these histories. However, it can be difficult to disentangle anthropogenic from non-anthropogenic dispersal in long-lived non-crop species. We developed a genomic workflow that can be used to screen out species that show patterns consistent with faunal dispersal or long-term isolation, and identify species that carry dispersal signals of putative human influence. We used genotyping-by-sequencing (DArTseq) and whole-plastid sequencing (SKIMseq) to identify nuclear and chloroplast Single Nucleotide Polymorphisms in east Australian rainforest trees (4 families, 7 genera, 15 species) with large (>30 mm) or small (<30 mm) edible fruit, either with or without a known history of use by Indigenous peoples. We employed standard population genetic analyses to test for four signals of dispersal using a limited and opportunistically acquired sample scheme. We expected different patterns for species that fall into one of three broadly described dispersal histories: (1) ongoing faunal dispersal, (2) post-megafauna isolation and (3) post-megafauna isolation followed by dispersal of putative human influence. We identified five large-fruited species that displayed strong population structure combined with signals of dispersal. We propose coalescent methods to investigate whether these genomic signals can be attributed to post-megafauna isolation and dispersal by Indigenous peoples.

Climate change threatens native potential agroforestry plant species in Brazil

Climate change is one of the main drivers of species extinction in the twentyfirst-century. Here, we  (1) quantify potential changes in species' bioclimatic area of habitat (BAH) of 135 native potential agroforestry species from the Brazilian flora, using two different climate change scenarios (SSP2-4.5 and SSP5-8.5) and dispersal scenarios, where species have no ability to disperse and reach new areas (non-dispersal) and where species can migrate within the estimated BAH (full dispersal) for 2041–2060 and 2061–2080. We then (2) assess the preliminary conservation status of each species based on IUCN criteria. Current and future potential habitats for species were predicted using MaxEnt, a machine-learning algorithm used to estimate species' probability distribution. Future climate is predicted to trigger a mean decline in BAH between 38.5–56.3% under the non-dispersal scenario and between 22.3–41.9% under the full dispersal scenario for 135 native potential agroforestry species. Additionally, we found that only 4.3% of the studied species could be threatened under the IUCN Red List criteria B1 and B2. However, when considering the predicted quantitative habitat loss due to climate change (A3c criterion) the percentages increased between 68.8–84.4% under the non-dispersal scenario and between 40.7–64.4% under the full dispersal scenario. To lessen such threats, we argue that encouraging the use of these species in rural and peri-urban agroecosystems are promising, complementary strategies for their long-term conservation.

Habitation Sites Influence Tree Community Assemblages in the Great Bear Rainforest, British Columbia, Canada

Identifying how past human actions have influenced their environment is essential for understanding the ecological factors that structure contemporary ecosystems. Intertidal resource use by Indigenous Peoples for thousands of years has led to habitation sites containing vast shell midden deposits and facilitating long-term impacts on soil chemistry and drainage. Here we examine how these shell middens have impacted various forest metrics, such as species diversity, community composition, canopy height, and regeneration recruitment to determine if forests on habitation sites differ from the surrounding matrix. We surveyed known habitation sites with archeological evidence indicating past year-round human occupation, within the Hakai Lúxvbálís Conservancy on Calvert and Hecate Islands within the Great Bear Rainforest along British Columbia’s Central Coast. Our results demonstrate that habitation sites exhibit lower tree species richness, less relative species abundances, as such, displayed lower Shannon diversity and inverse Simpson values. The composition of tree communities on habitation sites was statistically different, with western hemlock and western redcedar densities increasing on non-habitation sites. Conversely, regeneration diversity at habitation sites was more even and exhibited elevated Shannon diversity and inverse Simpson values. The community composition of regeneration was more consistent among habitation and non-habitation sites; however, western redcedar, western hemlock and Sitka spruce were more abundant at habitation sites. For all tree species, maximum height was higher within the habitation sites; however, this trend was the most notable in western redcedar and Sitka spruce, which increased by an average of 4.8 m relative to non-habitation sites. Collectively, our findings suggest that long-term habitation alters forest community compositions. The landscape alterations within habitation sites promote conditions needed to support diverse, even, and abundant regeneration communities and consequently increase the height of the dominant coastal tree species. Thus, our results offer evidence that long-term influence by Indigenous communities have a persistent influence on coastal forests.

Widespread homogenization of plant communities in the Anthropocene

Native biodiversity decline and non-native species spread are major features of the Anthropocene. Both processes can drive biotic homogenization by reducing trait and phylogenetic differences in species assemblages between regions, thus diminishing the regional distinctiveness of biotas and likely have negative impacts on key ecosystem functions. However, a global assessment of this phenomenon is lacking. Here, using a dataset of >200,000 plant species, we demonstrate widespread and temporal decreases in species and phylogenetic turnover across grain sizes and spatial extents. The extent of homogenization within major biomes is pronounced and is overwhelmingly explained by non-native species naturalizations. Asia and North America are major sources of non-native species; however, the species they export tend to be phylogenetically close to recipient floras. Australia, the Pacific and Europe, in contrast, contribute fewer species to the global pool of non-natives, but represent a disproportionate amount of phylogenetic diversity. The timeline of most naturalisations coincides with widespread human migration within the last ~500 years, and demonstrates the profound influence humans exert on regional biotas beyond changes in species richness.

Human-driven movements and extinctions of species have made plant communities across biomes more homogenous. Here the authors quantify plant vascular species and phylogenetic homogenization across the globe, finding that non-native species naturalisations have been a major driver.