Geographic isolation alone does not explain divergence of a group of orchid species across Brazil's campos rupestres sky-islandsIsolamento geográfico por si só não explica a divergência de um grupo de espécies de orquídeas nos campos rupestres do Brasil.

Mountains play a crucial role in the origin and maintenance of Neotropical biodiversity, but there are still unanswered questions about the diversification of the campos rupestres (CR), an herbaceous-shrubby sky-island vegetation in eastern South America. For orchids distributed across this disjunct rock habitat, difficulties with distinguishing morphological taxa add an additional challenge to disentangling the history of divergence. Here, we combined the power of ddRAD genomic data with broad sampling of Bulbophyllum sect. Didactyle (Orchidaceae), across the CR and other Neotropical outcrops, to estimate evolutionary relationships and evaluate the biogeography of the group's diversification. Although genetic lineages generally align with geographic disjunctions, we also observe distantly related lineages within some previously recognized species. For such taxa, their lack of monophyly and a shared regional divergence pattern suggests a complex history that may include unrecognized diversity. When viewed through the lens of morphological variability, our study raises intriguing questions about the persistence and permeability of species barriers among orchid populations. These results, in addition to the recency of the divergence history of B. sect. Didactyle, provide insights about hypothesized community level vs. species-specific paths of diversification across the Neotropical sky-islands of the CR.

Combining genotype, phenotype, and environmental data to delineate site-adjusted provenance strategies for ecological restoration.

Despite the importance of climate-adjusted provenancing to mitigate the effects of environmental change, climatic considerations alone are insufficient when restoring highly degraded sites. Here we propose a comprehensive landscape genomic approach to assist the restoration of moderately disturbed and highly degraded sites. To illustrate it we employ genomic data sets comprising thousands of single nucleotide polymorphisms from two plant species suitable for the restoration of iron-rich Amazonian Savannas. We first use a subset of neutral loci to assess genetic structure and determine the genetic neighbourhood size. We then identify genotype-phenotype-environment associations, map adaptive genetic variation, and predict adaptive genotypes for restoration sites. Whereas local provenances were found optimal to restore a moderately disturbed site, a mixture of genotypes seemed the most promising strategy to recover a highly degraded mining site. We discuss how our results can help define site-adjusted provenancing strategies, and argue that our methods can be more broadly applied to assist other restoration initiatives.

Range-wide neutral and adaptive genetic structure of an endemic herb from Amazonian Savannas.

Conserving genetic diversity in rare and narrowly distributed endemic species is essential to maintain their evolutionary potential and minimize extinction risk under future environmental change. In this study we assess neutral and adaptive genetic structure and genetic diversity in Brasilianthus carajensis (Melastomataceae), an endemic herb from Amazonian Savannas. Using RAD sequencing we identified a total of 9365 SNPs in 150 individuals collected across the species' entire distribution range. Relying on assumption-free genetic clustering methods and environmental association tests we then compared neutral with adaptive genetic structure. We found three neutral and six adaptive genetic clusters, which could be considered management units (MU) and adaptive units (AU), respectively. Pairwise genetic differentiation (F ST) ranged between 0.024 and 0.048, and even though effective population sizes were below 100, no significant inbreeding was found in any inferred cluster. Nearly 10 % of all analysed sequences contained loci associated with temperature and precipitation, from which only 25 sequences contained annotated proteins, with some of them being very relevant for physiological processes in plants. Our findings provide a detailed insight into genetic diversity, neutral and adaptive genetic structure in a rare endemic herb, which can help guide conservation and management actions to avoid the loss of unique genetic variation.

Chloroplast genomes of Byrsonima species (Malpighiaceae): comparative analysis and screening of high divergence sequences.

Byrsonima is the third largest genus (about 200 species) in the Malpighiaceae family, and one of the most common in Brazilian savannas. However, there is no molecular phylogeny available for the genus and taxonomic uncertainties at the generic and family level still remain. Herein, we sequenced the complete chloroplast genome of B. coccolobifolia and B. crassifolia, the first ones described for Malpighiaceae, and performed comparative analyses with sequences previously published for other families in the order Malpighiales. The chloroplast genomes assembled had a similar structure, gene content and organization, even when compared with species from other families. Chloroplast genomes ranged between 160,212 bp in B. crassifolia and 160,329 bp in B. coccolobifolia, both containing 115 genes (four ribosomal RNA genes, 28 tRNA genes and 83 protein-coding genes). We also identified sequences with high divergence that might be informative for phylogenetic inferences in the Malpighiales order, Malpighiaceae family and within the genus Byrsonima. The phylogenetic reconstruction of Malpighiales with these regions highlighted their utility for phylogenetic studies. The comparative analyses among species in Malpighiales provided insights into the chloroplast genome evolution in this order, including the presence/absence of three genes (infA, rpl32 and rps16) and two pseudogenes (ycf1 and rps19).