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Aim The Brazilian campo rupestre is a vegetation associated to ancient mountaintops in eastern South America, spread mainly over disjunct areas of the Espinhaço Range and the Chapada dos Veadeiros. These areas hold outstanding levels of plant diversity and endemism, but despite their uniqueness they have been neglected in recent bioregionalizations for the Neotropical region. Given their particular levels of species richness and endemism, we here test the recognition of these as distinct bioregions within the Chacoan dominion. Location Mountaintops of eastern South America. Methods We listed 1,748 angiosperm species endemic to the campo rupestre of the Espinhaço Range and Chapada dos Veadeiros regions, based on the data gathered from the Brazilian Flora 2020 Project. We extracted all occurrence information available from GBIF (the Global Biodiversity Information Facility) for such list and also for a polygon gathering all the study area, including information from adjacent vegetations. Data went through standard cleaning procedures and a network clustering analysis was performed to delimitate the boundaries of the new bioregions. Results Our data strongly support the recognition of two distinct bioregions along the Espinhaço Range, but none in the Chapada dos Veadeiros. Given their high levels of endemism and singularity within the Chacoan dominion, we formalize two provinces associated to campo rupestre in the Espinhaço Range, naming them as “Chapada Diamantina” and “Southern Espinhaço” provinces. Within the latter province, three districts are also recognized, based on this and previous studies: “Diamantina Plateau”, “Grão‐Mogol” and “Iron Quadrangle” districts. Main conclusions The formalization of new and previously described bioregions highlights the campo rupestre as a vegetation harbouring outstanding levels of species richness and endemism in South America, contributing to a better understanding of biogeographical patterns in the Neotropics. Also, as we follow the International Code of Area Nomenclature as a device to standardize recognition of bioregions, this shall facilitate further biogeographical and conservation studies in these areas. Further assessments with new and revisited data are needed to enable minor scale bioregionalization within the Chacoan dominion.

Cacao (Theobroma cacao), the primary source for chocolate manufacturing, is native to the Upper Amazon basin. It was introduced into Mesoamerica by pre‐Columbian societies and later spread globally following European colonization, becoming a commercially significant crop. Today, cacao populations exist along a continuum from wild to naturalized and cultivated forms across the Tropical Americas, complicating efforts to distinguish genuinely wild populations from those influenced by human activity. Here, we investigate genomic diversity, population structure, and domestication signals in three groups using RAD‐sequencing: Upper Amazonian populations (including Contamana, Marañón, Iquitos and Nanay), the Guiana population, and the Amelonado variety introduced into Eastern Brazil in the 18th century. The Upper Amazonian populations exhibited the highest genetic diversity and limited evidence of recent selection, reaffirming their role as the primary genetic source of cacao. The Amelonado group displayed signatures of artificial selection, including reduced genetic diversity and evidence of balancing selection, consistent with its introduction to Bahia before its later expansion to West Africa. The Guiana population showed intermediate genetic diversity and tight clustering but minimal differentiation from Upper Amazonian populations, suggesting they could represent an isolated wild lineage rather than an introduced group. These findings highlight the complexity of cacao's domestication history, shaped by multiple independent selection events and long‐term human influence. Understanding this continuum is important for unraveling the species' evolutionary history for supporting conservation and breeding strategies for cacao, a crop of major economic and cultural importance. Cacao populations span a continuum from wild to domesticated forms, shaped by complex patterns of human influence and selection. Using RAD‐sequencing, we show that native Upper Amazonian populations harbor the highest genetic diversity, while the Guiana group likely represents an isolated wild lineage and Amelonado shows clear signals of artificial selection. These findings clarify cacao's evolutionary history and support efforts in conservation and breeding.

Societal Impact Statement Biological samples and their associated information are an essential resource used by scientists, governments, policymakers, practitioners and communities to ensure that biodiversity can be appropriately protected and sustainably used. Yet, considering the enormous task of documenting the vast numbers of as‐yet‐unknown plant and fungal species, greater international coordination for biological collecting and recording is necessary, built on equitable collecting practices and standards. Here, we propose five commitments to accelerate and enhance scientific knowledge of plant and fungal diversity, while increasing collaboration, benefit sharing and efficiency. Summary Almost all life depends on plants and fungi, making knowledge of their diversity and distribution—primarily derived from biological collections—fundamental to national and international conservation, restoration and sustainable use commitments. However, it is estimated that some 15% of all plant species and over 90% of all fungal species have not yet been scientifically described, hampering our ability to assess and demonstrate the impact of efforts to halt biodiversity loss. In addition, organisations and researchers around the world lack a concerted strategy for increasing complementarity and avoiding overlap in botanical and mycological research, particularly in relation to the collection of specimens. We here present the 2030 Declaration on Scientific Plant and Fungal Collecting, summarising a commitment towards such a necessary strategy. Its components were identified from discussions during and after a series of four workshops and plenary discussions at the 2023 State of the World's Plants and Fungi symposium convened by the Royal Botanic Gardens, Kew, and were then consolidated into the present form by the authors. The Declaration was subsequently opened up for endorsement by signatories. Collectively, we agree on a set of five commitments for cataloguing the world's flora and funga, designed to maximise efficiency, facilitate knowledge exchange and promote equitable collaborations: (1) use evidence‐based collection strategies; (2) strengthen local capacity; (3) collaborate across taxa and disciplines; (4) collect for the future; and (5) share the benefits. This Declaration is a first step towards increased global and regional coordination of scientific collecting efforts. Biological samples and their associated information are an essential resource used by scientists, governments, policymakers, practitioners and communities to ensure that biodiversity can be appropriately protected and sustainably used. Yet, considering the enormous task of documenting the vast numbers of as‐yet‐unknown plant and fungal species, greater international coordination for biological collecting and recording is necessary, built on equitable collecting practices and standards. Here, we propose five commitments to accelerate and enhance scientific knowledge of plant and fungal diversity, while increasing collaboration, benefit sharing and efficiency.

Species occurrence records provide the basis for many biodiversity studies. They derive from georeferenced specimens deposited in natural history collections and visual observations, such as those obtained through various mobile applications. Given the rapid increase in availability of such data, the control of quality and accuracy constitutes a particular concern. Automatic filtering is a scalable and reproducible means to identify potentially problematic records and tailor datasets from public databases such as the Global Biodiversity Information Facility (GBIF; http://www.gbif.org ), for biodiversity analyses. However, it is unclear how much data may be lost by filtering, whether the same filters should be applied across all taxonomic groups, and what the effect of filtering is on common downstream analyses. Here, we evaluate the effect of 13 recently proposed filters on the inference of species richness patterns and automated conservation assessments for 18 Neotropical taxa, including terrestrial and marine animals, fungi, and plants downloaded from GBIF. We find that a total of 44.3% of the records are potentially problematic, with large variation across taxonomic groups (25–90%). A small fraction of records was identified as erroneous in the strict sense (4.2%), and a much larger proportion as unfit for most downstream analyses (41.7%). Filters of duplicated information, collection year, and basis of record, as well as coordinates in urban areas, or for terrestrial taxa in the sea or marine taxa on land, have the greatest effect. Automated filtering can help in identifying problematic records, but requires customization of which tests and thresholds should be applied to the taxonomic group and geographic area under focus. Our results stress the importance of thorough recording and exploration of the meta-data associated with species records for biodiversity research.

Digital accessible knowledge of biodiversity data is an increasingly important source of information in studies of biogeography and conservation. These databases can also reveal temporal, spatial and taxonomical gaps in biodiversity documentation, even in areas that have been intensively studied and from where accurate species lists are available. Therefore, revealing these gaps may help allocating collecting efforts, conservation priorities and strategies for improving database curation. Here, we evaluate potential shortfalls for flowering plants in a tropical hotspot, the Brazilian Atlantic Forest, by cross-referencing two online repositories of biodiversity data (the Global Biodiversity Information Facility – GBIF – and the Brazilian Flora 2020 floristic database – BFG). We aimed to evaluate the congruence between those repositories, highlighting tendencies in current documentation for this area. We found that from the 7220 reported flowering plant species endemics to the Atlantic Forest, 1573 (22%) have no valid spatial data in GBIF, and 75% of all of the 605,951 records do not present valid spatial information. Most of the missing information is related to species known only from few and old collections with absent or inaccurately georeferenced data. This lack of information may cause a large impact in spatial studies, especially for rare and threatened species. Nevertheless, our analysis also shows that spatial information for the filtered data is highly congruent between GBIF and BFG data, indicating relatively high availability of quality data in large repositories after standard and automatized cleaning procedures. Still, good practices to decrease the impact of losing data are recommended, including more investment in field collections, targeting poorly known species and returning cleaned spatial datasets to online repositories after taxonomic revisions.

Reticulate evolution (RE), involving hybridization and related processes, generates network-like rather than strictly bifurcating relationships among lineages and can obscure phylogenetic relationships. Detecting ancient hybridization is particularly challenging, as genomic signals may erode over time. The Malvatheca clade (Malvaceae), marked by multiple paleopolyploidy events since it’s estimated origin 66 my, offers a useful model for examining RE. Its three subfamilies—Bombacoideae (with high chromosome numbers, mostly trees), Malvoideae (lower chromosome numbers, mostly herbs), and the recently described Matisioideae—show unresolved relationships, with several taxa of uncertain placement. We conducted a phylogenomic analysis of 69 Malvatheca species via complete plastomes, 35S rDNA cistrons, nuclear low copy genes and comparative repeatome data. Most of the datasets consistently resolved four clades: (I) Bombacoideae, (II) Malvoideae, (III) Matisioideae, and (IV) a heterogeneous assemblage including representatives of Malvoideae, Matisioideae and several incertae sedis taxa. Chromosome numbers were negatively correlated with repeatome diversity: Bombacoideae presented higher counts but lower repeat diversity, possibly reflecting slower repeat evolution associated with woody growth forms. In contrast, clades III and IV showed marked heterogeneity in both chromosome number and repeat composition, which is consistent with a reticulate origin. Overall, our results show evidence of ancient hybridization and polyploidy in shaping Malvatheca evolution. These results highlight that reticulation and genome dynamics, rather than taxonomic boundaries alone, are central to understanding the diversification of Malvatheca.

Seasonally dry tropical forests (STDFs) are a main component of open seasonally dry areas in South America and their biogeography is understudied compared to evergreen forests. In this work, we identify vascular plant species with long-distance disjunctions across STDF patches of South America based on information available in online repositories and on species taxonomy and distribution, to explore species’ biogeographic patterns. Specifically, we combine distribution data from the Brazilian Flora 2020 Project (BFG) and the Global Biodiversity Information Facility (GBIF) to identify species with a peri-Amazonian distribution, and then use species distribution models to discuss possible scenarios of peri-Amazonian distributions under Pleistocene climatic fluctuations. We identified 81 candidate species for peri-Amazonian distributions in STDFs, including shrubs, herbs, trees and lianas, and provided a summary of their main fruit dispersion syndrome based on the literature to identify prevalent dispersal patterns. The study species responded differently to Pleistocene climatic fluctuations, with both contractions and expansions through time in different rates and do not show consistent larger distributions during past climate conditions. Our results show that a peri-Amazonian distribution is also present in growth-forms other than trees. Also, the prevalence of species with long-distance dispersal strategies such as wind or vertebrate-dispersed can suggest, although biased for Neotropical taxa, an alternative scenario of long-distance dispersal, possibly using stepping-stones of azonal vegetation. We argue that such an alternative scenario, especially for species disjunct with long-dispersal abilities, should be considered to test if STDF disjunctions are relics of a past widespread distribution or not.

Amazonia, one of the largest and most biodiverse ecosystems on Earth, is a significant yet less-known arena for ancient plant domestication. Here, we traced the origins of cupuaçu ( Theobroma grandiflorum ), an Amazonian tree crop closely related to cacao ( T. cacao ), cherished for its flavorful seed-pulp, by employing an extensive genomic analysis based on data from four sites in Brazil. Our results indicate that cupuaçu is a domesticated variant of its wild relative, cupuí ( T. subincanum ), probably originating from the Middle-Upper Rio Negro basin. A first phase of domestication is observed through a genetic bottleneck that we estimated to have occurred 5000–8000 years before the present. Moreover, we found further reductions in genetic diversity that we estimated to have occurred during the modern era. This is consistent with a second phase of domestication that was accompanied by an increase in the geographic distribution of cupuaçu over the last two centuries. Unraveling cupuaçu ’s origins adds it to the roster of plants domesticated by Amazonian indigenous people in the early to mid-Holocene. Our results suggest that Amazonia’s current patterns of genetic diversity and distribution of domesticated plants were influenced by both pre-Columbian and modern histories.

Species from the \"cacao group\" are traditionally allocated into two genera, Theobroma and Herrania (Malvaceae, Byttnerioideae), both groups of Neotropical species economically relevant, such as the cacao tree ( Theobroma cacao ), which forms the source of chocolate. This study aimed at compiling and describing a dataset of preserved specimen collections available in the Global Biodiversity Information Facility repository (GBIF) for Tropical Americas. Data were exhaustively revisited and analysed in terms of taxonomic identity, conditions of collection and georeferencing, all of which should enable downstream taxonomic, geographic and evolutionary analyses. Our dataset compiles 7975 records of preserved specimen collections found at herbaria. Records are from 18 species of Theobroma and 14 of Herrania , occurring in 60 countries or major territories, with two species endemic to a single country ( H. kofanorum from Ecuador and H. laciniifolium from Colombia). Occurrence records are mostly restricted to the Amazon rainforest and species with more occurrence records are cupuí , T. subincanum (1535 records), followed by the cacao tree, T. cacao (1500 records), the latter having cultivated specimens in Africa, Asia and Oceania. In the case of the genus Herrania , H. nitida and H. purpurea are the species with the majority of occurrences (respectively, 431 and 273 records). Most of the botanical samples from these genera are found in American, Brazilian and Colombian collections, with a particular strength for American herbaria. We describe how occurrence records are spread spatially and temporally and highlight key field expeditions responsible for enhancing most of the knowledge of cacao and its wild relatives, especially in countries where they prevail, such as Colombia (with 29 species), Ecuador (23 species), Brazil (18 species) and Peru (15 species). Specifically, expeditions in these countries were led by American and European initiatives in conjunction with local funding in the mid-20 th century. We emphasise how initiatives of such kind seems to have weakened in the 21 st century and most of the collections of Theobroma and Herrania made afterwards are from various collectors that seek to resample specimens in already explored sites.

Cacao (Theobroma cacao, Malvaceae) is an important tree crop in Africa and in the Americas. Current genomic evidence suggests that its original range in Tropical Americas was smaller than its current distribution and that human-mediated dispersal occurred before European colonization. This includes regions like Mesoamerica and Eastern Amazonia where cacao is supposedly naturally occurring. In this study, we utilize remote sensing and land use data to examine the influence of human activities on cacao-growing regions and explore patterns between cacao distribution and anthropized areas. By evaluating nearly nine thousand preserved specimen collections, we worked with a comprehensive occurrence dataset that considers taxonomy and distribution. We then analyzed remote sensing images of specimen locations and compared land use profiles of regions into which cacao was introduced with documented native areas. Our findings revealed a clear association between anthropized areas and cacao specimens, with the majority located in areas strongly affected by human activities. Conversely, regions closer to the proposed native range of cacao exhibit less human impact. These results, while accounting for sampling bias, reinforce the idea that humans may have played a significant role in cacao’s dispersal, even in parts of the Amazon where its native status remains uncertain. The discussion on cacao’s native range and identification of introduced areas hold implications for jurisdiction, access to genetic resources, and conservation efforts. Additionally, it is relevant to debates surrounding the repatriation of genetic data of economically important crops. Understanding the historical human influence on cacao’s distribution is crucial for addressing issues of crop improvement, conservation, and sustainable use.