Chloroplast genomes are considered to be highly conserved. Nevertheless, differences in their sequences are an important source of phylogenetically informative data. Chloroplast genomes are increasingly applied in evolutionary studies of angiosperms, including Magnoliaceae. Recent studies have focused on resolving the previously debated classification of the family using a phylogenomic approach and chloroplast genome data. However, most Neotropical clades and recently described species have not yet been included in molecular studies. We performed sequencing, assembly, and annotation of 15 chloroplast genomes from Neotropical Magnoliaceae species. We compared the newly assembled chloroplast genomes with 22 chloroplast genomes from across the family, including representatives from each genus and section. Family-wide, the chloroplast genomes presented a length of about 160 kb. The gene content in all species was constant, with 145 genes. The intergenic regions showed a higher level of nucleotide diversity than the coding regions. Differences were higher among genera than within genera. The phylogenetic analysis in Magnolia showed two main clades and corroborated that the current infrageneric classification does not represent natural groups. Although chloroplast genomes are highly conserved in Magnoliaceae, the high level of diversity of the intergenic regions still resulted in an important source of phylogenetically informative data, even for closely related taxa.

Mexico's extraordinary tree diversity is threatened by the increasing demand for resources because of the tenfold population growth in the last century. The conservation status of trees and both urban and rural livelihoods are also negatively affected by agriculture, mining and tourism. Nearly 60% of the Mexican endemic and near endemic tree species whose conservation status we have assessed for the Red List of the International Union for Conservation of Nature are threatened, almost double the percentage of threatened trees worldwide. If no measures are taken to protect this tree diversity properly, these resources will be forever lost for human sustainability. Summary• Mexico is floristically the fourth most species-rich country in the world. Currently, 3620 native tree species are reported from this country. Mexico has been a forerunner at global level in recognising the need for plant conservation, yet this is in stark contrast with governmental programmes and actions, past and present that negatively affect(ed) immense areas of primary vegetation. In the framework of the Global Tree Assessment, to date, we have assessed the conservation status of nearly 1500 Mexican endemic and near endemic tree species for the International Union for the Conservation of Nature (IUCN) Red List, the distribution data of which we use here for a first meta-analysis of conservation statuses and spatial distribution patterns in a newly delimited area we call Natural Mexico.• Our database consists of 112,416 taxonomically and geographically very carefully curated distribution points of 1474 tree species endemic to Mexico and adjacent areas, belonging to 98 flowering plant families. The extensive curation methodology we consider essential for both research and conservation purposes is emphasised.

The Mexican state of Veracruz has suffered very high deforestation rates in the last few decades, and despite the establishment of protected areas and conservation projects, primary forest is now mainly persisting in mostly small, scattered, fragmented remnants. New species of Magnolia section Talauma in this state have been described with little to no reference to the already existing ones, potentially resulting in over-splitting, obscuring their taxonomic delineation and conservation status, and consequently conservation programs. To study the conservation units and their genetic diversity, we here employ 15 microsatellite markers on a highly representative sampling of 254 individuals of what are presumed to be five Magnolia species. The results support at least three species and maximum five main conservation units. We propose downgrading the latter to four, given morphological, ecological, demographical, and geographical considerations. Two out of the three sympatrically occurring species in the rainforest in the Los Tuxtlas volcanic area have weak genetic evidence to be considered separate species. Similarly, the individuals in the Sierra de Zongolica in central Veracruz, who bear a very high morphological and genetic similarity to Magnolia mexicana, have weak genetic evidence to be recognised as a separate species. Nonetheless, the individuals could be identified as Magnolia decastroi based on morphology, and further research including the full range of this species is recommended.