Matias Köhler

The emergence of conflicting signals among different genomic regions, individual genes, and inference methods has been frequently reported in phylogenomic studies. Conflicts can occur from methodological error and biological processes, and disentangling the contribution of each putative source of discordance became a major challenge. Here, we assembled a dataset of 684 low‐copy nuclear markers from genome skimming data to build a phylogeny of Melastomataceae. The primary goal of this paper was to evaluate the phylogeny backbone regarding conflict across tribal relationships. To this end, we further investigated putative sources driving phylogenetic conflicts and uncertainty, including incomplete lineage sorting, nucleotide evolutionary rate heterogeneity, lack of information, inference error, and gene flow. The phylogenetic hypotheses of Melastomataceae estimated here (concatenated and coalescent) have corroborated the recurrent pattern found across several studies, in which major clades (subfamilies and tribes) have high support and a stable composition, but uncertainty is recovered for the relationships among some of them. The power of our explanatory variables for gene tree variation was effective to explain the variation in the backbone nodes. Inference error was the predictor explaining most of the variance found, a scenario that could be linked with an ancient rapid radiation in the family. The second most important predictor to explain gene tree variation was the ratio between the rates of molecular evolution of genes supporting a node versus conflicting signal. The signal of this predictor was particularly high in the node describing the sister relationship of two subfamilies (Olisbeoideae and Kibessioideae), indicating that long‐branch attraction artifacts might be affecting this deep relationship. Ancient gene flow was not estimated as a major factor driving backbone node uncertainty, but some signal of ancient introgression was recovered for specific nodes associated with a “hotspot” of conflicting relationships involving several tribes. Our analyses point to a scenario where lack of information does not seem to explain tribal relationship uncertainties with the data at hand. Therefore, attention should be given to better analyzing the molecular data available, especially with the emergence of new methodologies.

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.

A phylogenetic study of Uebelmannia investigates the relationships of a newly discovered taxon in this enigmatic, early‐diverging genus that is sister to all the other c. 460 species of tribe Cereeae. Here we present a coalescent‐based phylogenetic tree inferred with nuclear genes captured by the Cactaceae591 probe set encompassing all Uebelmannia species. The new taxon U. nuda is sister to U. pectinifera, while U. gummifera and U. buiningii form another pair of closely related species. The unusual characteristics of the new cactus (semi‐subterranean/geophytic habit, turbinate stem, naked areoles) distinguish it from all other Uebelmannia species. The definition of the relationships within this early‐derived genus endemic to the campo rupestre of Minas Gerais State became more evident, and this new find adds to the importance of this biogeographic province for the evolution of tribe Cereeae. The new species is described, and a preliminary conservation assessment is presented. Additionally, a key for all taxa of the genus is provided.

Cerrado is a large and heterogeneous ecoregion in the Neotropics marked by the fire‐prone savanna vegetation, to which succulent lineages are usually not associated due to this adverse condition. However, recent studies have highlighted the importance of Cerrado as an ancestral range for the origin, dispersal and in situ diversification of remarkable lineages of South American cacti. In this perspective, we explore the implications of these occurrences in the Cerrado, shedding light on a frequently overlooked aspect of this ecoregion—the role of scattered rocky outcrop habitats acting as micro‐refuges for fire‐sensitive lineages. We show that most cacti occurrences are associated with patches of rock outcrops across the Cerrado. In contrast, when terricolous, a few disparate and not closely related species can develop underground structures or present a specialized habit that facilitates their presence as a putative response to fire—reinforcing the evolutionary lability of fire adaptation in Cerrado lineages. Despite some notable endemisms, several occurrences are from species with core distributions in adjacent ecoregions (e.g. Caatinga and Chaco), demonstrating the permeability of Cerrado, which can act concomitantly as a biogeographical barrier (especially due to its fire‐prone habitats) and as a corridor for biota interchange. Finally, we stress that Cerrado heterogeneity, often leading to different circumscriptions, is a relevant issue when studying and characterizing Neotropical biota, which must be further explored and considered to assess the evolutionary assembly of the biomes involved.

Plastid genomes (plastomes) have long been recognized as highly conserved in their overall structure, size, gene arrangement and content among land plants. However, recent studies have shown that some lineages present unusual variations in some of these features. Members of the cactus family are one of these lineages, with distinct plastome structures reported across disparate lineages including gene losses, inversions, boundary movements, or loss of the canonical inverted repeat (IR) region. However, just a small fraction of cactus diversity has been analyzed so far. Here, we further investigated plastome features of the tribe Opuntieae, the remarkable prickly pear cacti, which represent one of the most diverse and important lineages of Cactaceae. We de novo assembled the plastome of 43 species, representing a comprehensive sampling of the tribe including all seven genera, and analyzed their evolution in a phylogenetic comparative framework. Phylogenomic analyses with different datasets (full plastome sequences and just genes) were performed, followed by congruence analyses to assess signals underlying contentious nodes. Plastomes varied considerably in length from 121 kbp to 162 kbp, with striking differences in the content and size of the IR region (contraction and expansion events), including the lack of the canonical IR in some lineages, and the pseudogenization or loss of some genes. Overall, nine different types of plastomes were reported deviating in the presence of the IR region or the genes contained in the IR. Overall, plastome sequences resolved phylogenetic relationships within major clades of Opuntieae with high bootstrap values but presented some contentious nodes depending on the data set analyzed (e.g., whole plastome vs. genes only). Congruence analyses revealed that most plastidial regions lack phylogenetic resolution, while few markers are supporting the most likely topology. Similarly, alternative topologies are driven by a handful of plastome markers, suggesting recalcitrant nodes in the phylogeny. Our study reveals a dynamic nature of plastome evolution across closely related lineages, shedding light on peculiar features of plastomes. Variation of plastome types across Opuntieae is remarkable in size, structure, and content, and can be important for the recognition of species in some major clades. Unraveling connections between the causes of plastome variation and the consequences on species biology, physiology, ecology, diversification, and adaptation, is a promising and ambitious endeavor in cactus research. Although plastome data resolved major phylogenetic relationships, the generation of nuclear genomic data is necessary to confront these hypotheses and further assess the recalcitrant nodes.

The formation of the western North American drylands has led to the evolution of an astounding diversity of species well adapted for such communities. Complex historical patterns often underlie the modern distribution of the flora and fauna of these areas. We investigated the biogeography of a group of desert-adapted prickly pears, known as the Xerocarpa clade, from western North America. The Xerocarpa clade originated in the mid-late Pliocene, likely on the Colorado Plateau, and then moved south into the Mojave, Sonoran, and Chihuahuan deserts, and California montane regions, further diversifying, mostly into the Quaternary. The southward trajectory of the clade was likely greatly influenced by the formation of the Grand Canyon. The synapomorphy of dry fruit presumably impeded the long-distance dispersibility of the beavertail cactus, Opuntia basilaris, while dry, spiny fruit may have enabled O. polyacantha to substantially increase its distribution. Opuntia basilaris evolved a pubescent epidermis, allowing it to invade hotter, drier conditions, while the spine-clothed stems of O. polyacantha may have given it an advantage for increasing its northern range into colder environments. The Xerocarpa clade shows a cold desert origin, and changes in morphological characters have made these sister taxa well adapted for invading broadscale, but oftentimes contrasting habitats.