Mariana Cosse

Floras and botanical collections are essential tools for understanding plant diversity, promoting its conservation, and supporting a wide range of scientific applications. Uruguay, located in the biodiverse grassland region of southern South America, has had only an incomplete Flora, the most comprehensive of which was published more than a century ago. We review the country's flora and the history of its study, and introduce the new Flora Uruguaya Online (FUO; https://florauruguaya.org ), which when completed will provide a comprehensive record of all vascular plant species, including information on their distribution, morphological, ecological, and phenological characteristics. This online Flora presently contains information on 182 families, 1053 genera, and 3112 species, 85.4% of which are native to Uruguay and 2.2% endemic. Although Uruguay accounts for only 25% of the surface area of the Río de la Plata Grasslands, it contains over 60% of their species and more than 50% of their endemic taxa, reflecting its core geographical position. Uruguay's flora faces increasing pressure from land‐use change, habitat fragmentation, and invasive species. FUO provides critical support for addressing these challenges, offering systematic botanical data for basic and applied research, conservation, sustainable uses, and land management, including practical applications such as the identification of toxic plants affecting livestock production. We highlight key features of FUO with its research‐enabling tools for the exploration of Uruguay's botanical richness by scientists, as well as by policymakers, educators, conservationists, and citizens. These features include its accessibility, interactivity, multiple filters (e.g., geographic regions, ecological characteristics, conservation status, or specific species attributes), rich graphics, and multiple sources of data inputs tied to herbarium specimens.

Sandy beaches are dynamic ecosystems supporting diverse life forms and remain less explored in terms of biodiversity compared to other coastal systems. Environmental DNA (eDNA) coupled with sequencing technology has emerged as a non-invasive method for assessing biodiversity, particularly in understudied habitats such as sandy beaches. This study employed eDNA metabarcoding on sediments from four Uruguayan beaches (two urban and two rural) using 18S and COI markers to assess the eukaryotic diversity of eDNA found in sandy beaches. Sediments were collected from the intertidal zone, and DNA was extracted. PCR products were then obtained and subsequently sequenced using high-throughput methods. Taxonomic diversity was analyzed at the family level, categorizing molecular operational taxonomic units (MOTUs) into ecological groups (e.g. algae, fungi, benthos). The 18S marker identified 67% of MOTUs, outperforming the COI marker, particularly for algae, fungi, and microbenthos. Algae had the highest diversity (in terms of the number of MOTUs), followed by microbenthos and fungi, while parasites and zooplankton had fewer MOTUs detected. Beaches showed no clear eDNA diversity differences, although site-specific variations in MOTUs abundance were noted. Some taxa, such as harmful algae and pathogens, have both ecological and health significance. These results demonstrate the utility of eDNA in revealing the diversity of sandy beach DNA and detecting taxa of ecological concern. Expanding spatial and taxonomic coverage, increasing the number of samples, and refining methodologies could further enhance our understanding of biodiversity patterns in these ecosystems.

A taxonomic revision of Austroeupatorium in Uruguay is presented. We provide expanded descriptions, photos, maps, and a key for the identification of Austroeupatorium species from this country. The genus is represented by three species: the widespread A. inulifolium; A. laetevirens, which represents a new formal record; and A. steviifolium, here proposed as a new combination in the genus based on Eupatorium steviifolium, which also represents a new record. Frequent misidentifications and affinities with other similar genera and species are discussed.

The loss of biodiversity has accelerated during the Anthropocene era, matching rates seen in previous mass extinctions (Rockström et al., 2009), resulting in unprecedented environmental changes (IPBES, 2021). In this scenario, it is crucial to make progress in effectively describing, documenting, and classifying living species. Acknowledging this urgency, the Convention on Biological Diversity (CBD) has highlighted the essential role of taxonomy in achieving these goals (CBD, 2021). However, human resources with expertise in taxonomy are increasingly scarce and often face intricate challenges like identifying cryptic species and larval stages (Thomsen et al., 2015). These challenges have sparked a need for alternative approaches in biodiversity description and monitoring. In response, Barcodes of Life (BoL) have emerged to identify organisms through genomic approaches utilizing specific DNA regions and standardized protocols (Hebert et al., 2003). The potential of this strategy has been demonstrated on a global scale as a powerful tool, with widespread applications including natural resource conservation, safeguarding endangered species, agricultural pest management, disease vector identification, water quality surveillance, verification of health and food products, forensic entomology, as well as medicinal plant identification, among others (Consortium for the Barcode of Life, 2007).DNA techniques require the meticulous selection of suitable barcoding regions, involving the identification of standardized loci that can be systematically and reliably sequenced across extensive and diverse taxa. This enables the generation of easily comparable data that facilitates species distinction (Hollingsworth et al., 2011). In animals, cytochrome oxidase I (COI) is the standard DNA barcode, showing notable success in precisely identifying species (Hebert et al., 2003). However, identifying an equivalent DNA barcode for plants remains challenging due to the absence of a single, appropriate locus for species delimitation (Hebert et al., 2016). Plant DNA barcoding has been controversial due to the presence of hybridization, introgression processes, and polyploidy (Hebert et al., 2016). The slow evolutionary rate in plant mitochondrial genomes rules out COI as a universal plant barcode (Hollingsworth et al., 2011). Instead, several chloroplast and nuclear molecular markers like rbcL, matK, trnH-psbA, trnL (UAA), and ITS have been explored as viables alternatives (Hollingsworth et al., 2011;Taberlet et al., 2007;Marcial-Quino et al., 2015). Given the inadequate species discrimination in certain plant groups with a single molecular marker, a combination of markers has been proposed (Hollingsworth et al., 2011).Another central aspect for taxa recognition using molecular markers is the need for a comprehensive reference database of barcode DNA sequences encompassing a wide range of species (Hollingsworth et al., 2011;Tnah et al., 2018). The quantity of sequences accessible for a specific locus impacts its discriminatory power (Hollingsworth et al., 2011). Establishing a robust public sequence repository is essential for assessing multiple potential loci for barcoding and their combination (Hollingsworth et al., 2011;Kolter and Gemeinholzer, 2021).Based on these principles, the Consortium for the Barcode of Life (CBoL; www.barcodeoflife.org) was established and is collaboratively building the Barcode of Life Data Systems (BOLD, Ratnasingham et al., 2007;www.boldsystems.org). BOLD is a global open access repository of DNA barcodes, but unlike other public genomic repositories such as GenBank (NCBI), EMBL, and DDBJ, it is specifically tailored for biodiversity and species identification through DNA barcoding (Borisenko et al., 2009), linking morphological and distributional data with DNA sequences. It also supports broader taxonomic initiatives such as the Global Taxonomic Initiative (GTI) for the Convention on Biological Diversity (CBD) and the Global Biodiversity Information Facility (GBIF) (Costa and Antunes, 2012).Among the vast array of over 375,000 documented vascular plant species worldwide (Hong et al., 2022), only 115,768 are registered within BOLD's database with a total of 380,813 public records (BOLD, 22/04/2024). This underscores the pressing necessity for substantial contributions from diverse researchers, institutions, and national networks to enhance the comprehensiveness of this database.In recent years, Uruguay has experienced a decline in biodiversity, a global phenomenon impacting ecosystems worldwide. The dramatic shifts in land use since the 1990s, particularly marked by an increase in the area of tree plantations (the highest in South America) and agriculture (specifically soybean and rice), underscore the urgent need for effective advances in documenting and categorizing the country's biodiversity (Paruelo et al., 2006, Baeza et al., 2020). Currently, vascular plants in Uruguay remains largely unexplored in terms of barcode sequence availability. The BOLD platform holds 1,131 public records for Uruguayan organisms, representing 323 species, with only 24 vascular plant species documented (searched on 22/3/2024), which accounts for less than 1% of native species reported for the country (Bonifacino et al., 2019). As a way of filling this void of DNA barcode sequences among the Uruguayan biodiversity, a major initiative is underway to establish a DNA barcode national network. During October 2018 the "Barcode of Life Training Course: example from native flora" was held, under the call for the program "Filling the capacity gap for the application of DNA technologies in taxonomy -GTI trainings/workshops driven by the trained trainers". This project had two main objectives: i) to train undergraduate and postgraduate students, as well as technicians from public and private institutions; to conduct workshops with vascular plant specialists to list key species of the Uruguayan flora;...

Although only a few species of Tuber account for the major truffle sales volume, many species that are not considered delicacies are finding their way to the market, especially in regions where the traditionally appreciated ones do not occur. This is the case for whitish truffles. Specimens of whitish truffles were collected in pecan (Carya illinoinensis) orchards in Uruguay in October 2021. Morphological and molecular methods were used to characterize and assess their identity as Tuber maculatum Vittad. An SPME extraction of volatile compounds and GC–MS analyses were performed to characterize the aromatic profile of these specimens and evaluate their potential applications. Among the 60 VOCs detected, 3-octenone (mushroom odor), 3-octanol (moss, nut, mushroom odor), and 2H-pyran-2-one (no odor), followed by octen-1-ol-acetate (no odor) and 2-undecanone (orange, fresh, green odor) were the major compounds in T. maculatum fruiting bodies. The attributes of exotic edible mushrooms of commercial value in the region are highlighted. In particular, this work emphasizes the characteristics of truffles as a byproduct of pecan cultivation.

Pampas and crab-eating foxes are medium-sized canids living in sympatry in the middle east of South America. Studies on the diet composition of these species provide a deep understanding of their ecological roles in the ecosystem structure and regulation. Using the metabarcoding technique, we analyzed the diet of both fox species in order to identify the vertebrate taxa included as food items. A fragment of the 12S ribosomal gene of the mtDNA was amplified using DNA extracted from 27 scat samples collected in south-central Uruguay during cold (June 2015) and warm (January – April 2016) seasons. A fox DNA blocking primer was designed to minimize the host amplicon products, and pooled samples were sequenced through paired-end reads (100 bp library) on a MiSeq Illumina Platform. The generated sequences were compared to a reference database built with sequences available in GenBank. In concordance with previous studies using traditional methods, we found that the most common food taxon were rodents. Qualitative differences in diet composition between both fox species were identified. Armadillo species were only found in pampas fox diet, while a greater variety of amphibians and birds were detected in crab-eating fox feces. Additionally, an innovative approach to differentiate between real and artifact sequences was employed. This method was based on comparing mutations at conserved and non-conserved positions within the secondary structure of the 12S rRNA, combined with network sequence reconstruction. Our results demonstrate the efficacy of the methodology in detecting the food species present in both fox diets, enabling the evaluation of intraspecific diversity among these species and facilitating the discarding of sequencing errors. This makes the methodology applicable to a wide range of studies.

In this study, we explore the applicability of DNA barcoding, specifically targeting the chloroplast DNA (cpDNA) sequences, particularly the trnL (UAA) intron region, to analyze the diet of gray brocket deer. This approach offers improved taxonomic resolution and the ability to identify species with greater precision compared to traditional methods. The study was conducted in the "Reserva Natural Salus" in Uruguay, covering a range of vegetation types, where gray brocket deer coexist with other exotic ungulates. A local reference database of trnL (UAA) sequences was established, incorporating both GenBank data and sequences obtained from native species in the study area. Fecal samples were collected in summer and winter, and DNA was extracted and amplified for metabarcoding analysis in pooled samples for each season. For each sample 28,229 and 33,588 reads were obtained respectively, which together corresponded to 25 Operational Taxonomic Units (OTUs). The species Rubus ulmifolius and Schinus engleri were the most represented in the diet with 69.6 % of the summer reads, whereas in winter, 68.7 % of the reads corresponded only to Schinus engleri. These findings indicate that gray brocket deer consume species that have higher nutritional value, which may be linked to their capacity to thrive in young and productive ecosystems. This study demonstrates the feasibility of DNA barcoding for dietary analysis in gray brocket deer and provides valuable insights into their food habits in the "Reserva Natural Salus". Further improvements to increase the reference databases of native species and the exploration of additional genetic markers are recommended for enhanced species-level discrimination in dietary analysis studies. This methodology is promising for future research as diet studies have an impact on species management, habitat conservation and biodiversity conservation efforts.

The Pampas deer (Ozotoceros bezoarticus) is a unique species of neotropical cervid, that inhabits a wide range of open habitats including grasslands, pampas, savannas, and cerrado (Brazil) from -5° to -41° S. The reduction of the area encompassed by these habitats has been dramatically reduced to less than 2 % by human activities such as agriculture, urbanization, and poaching. Three decades ago, we initiated a molecular genetic study of the Pampas deer based on representative samples from throughout their geographic range. Our aim is to reevaluate the effect that habitat fragmentation has had on gene flow among eight wildlife Pampas deer populations and one from the captive breeding centre Estación de Cría de Fauna Autóctona (ECFA). We examined DNA sequences from three mitochondrial markers: the control region (D-loop), Cytochrome b (Cytb), and Cytochrome Oxidase I (COI). Furthermore, we compared the resolution of the different mitochondrial markers to elucidate the phylogenetic and phylogeographic patterns of the species to define Evolutionary Significant Units (ESU`s). The amount of gene flow was correlated with geographic distance among groups and populations and was consistent with limited dispersal being the primary determinant of genetic differentiation between populations. Our results showed that the D-loop was the most appropriate marker for defining Evolutionary Significant Units. We found that the critically endangered Paraná population showed significant genetic distance from the others and revealed unique haplotypes with all the mitochondrial markers. The molecular genetic results provide a mandate for habitat restoration and design a management plan to conserve these relictual populations.