Mexico is considered an exceptional biogeographic area with a varied endemic flora, however spatial phylogenetic measures of biodiversity have not yet been estimated to understand how its flora assembled to form the current vegetation. Patterns of species richness, endemism, phylogenetic diversity, phylogenetic endemism and centers of neo-and paleo-endemism were determined to examine differences and congruence among these measures, and their implications for conservation. Of 24 360 vascular plant species 10 235 (42%) are endemic. Areas of endemism and phylogenetic endemism were associated with dry forests in zones of topographic complexity in mountain systems, in deserts, and in isolated xeric vegetation. Every single locality where seasonally tropical dry forests have been reported in Mexico was identified as an area of endemism. Significant phylogenetic diversity was the most restricted and occurred in the Trans-Mexican Volcanic Belt and in the Sierra de Chiapas. Notably, the highest degree of phylogenetic clustering comprising neo-, paleo-, and super-endemism was identified in southernmost Mexico. Most vascular plant lineages diverged in the Miocene (5-20 mya) when arid environments expanded across the world. The location of Mexico between two very large landmasses and the fact that more than fifty percent of its surface is arid favored the establishment of tropical lineages adapted to extreme seasonality and aridity. These lineages were able to migrate from both North and South America across Central America presumably during the Miocene and to diversify, illustrating the signature of the flora of Mexico of areas of endemism with a mixture of neo-and paleo-endemism.

Traditional agave spirits such as mezcal or tequila are produced all over Mexico using different species of Agave. Amongst them, A. angustifolia is the most popular given its agricultural extension. A. angustifolia is a wild species extensively distributed from North to Central America, and previous studies show that it is highly related to the tequila agave A. tequilana. In different regions of Mexico, A. angustifolia is cultivated under different types and levels of management, and although traditional producers identify several landraces, for the non-trained eye there are no perceivable differences. After interviews with producers from different localities in Jalisco, Mexico, we sampled A. angustifolia plants classified as different landraces, measured several morphological traits, and characterized their genetic differentiation and diversity at the genome-wide level. We included additional samples identified as A. tequilana and A. rhodacantha to evaluate their relationship with A. angustifolia. In contrast with previous studies, our pool of ca 20K high quality unlinked SNPs provided more information and helped us to distinguish different genetic groups that are congruent with the ethnobotanical landraces. We found no evidence to genetically delimitate A. tequilana, A. rhodacantha and A. angustifolia. Our large genome level dataset allows a better understanding of the genetic identity of important A. angustifolia traditional and autochthonous landraces.

Aim To test hypotheses on the origin and assembly of the flora of the Chihuahuan Desert using as a system the hard‐leaved shrubby lineages of the Rosaceae distributed in North American Deserts. Location North American Deserts, Chihuahuan Desert, Mexican Plateau, Tehuacán Valley. Taxa Rosaceae, Amygdaloideae (Amelanchier paniculata, Lindleya mespiloides, Malacomeles denticulata, Vauquelinia angustifolia, Vauquelinia australis, Vauquelinia corymbosa, Xerospiraea hartwegiana), Dryadoideae (Cercocarpus fothergilloides, Cercocarpus pringlei, Cercocarpus rzedowskii, Purshia plicata) Methods Phylogenetic analyses were conducted based on nine chloroplast and nuclear molecular markers of eleven newly sequenced species of Rosaceae distributed in the Chihuahuan Desert along with previous sequences of 41 species in 25 genera representative of the major clades in the family. Based on phylogeny, divergence times, migration, vicariance events and ancestral biogeographic areas were determined. Ecological niche‐based modelling will predict changes in distribution during Pleistocene climate oscillations. Traitgrams were constructed to visualize departure among lineages in the most significant climate variables. Results The lineages studied diverged during the Eocene‐Oligocene (53–33 Mya). The ancestral area for most of the taxa was in the Mojave and Chihuahuan Deserts. Most dispersal events occurred from the Mojave Desert to the central area of the Chihuahuan Desert on the Mexican Plateau. Ecological niche‐based modelling suggests a contraction of suitable habitat during the Last Interglacial period (~120,000–140,000 years), followed by expansion during the Last Glacial Maximum (~22,000 years) and the Middle Holocene (~6,000 years). Main conclusions Our results confirm the Axelrod's hypothesis of an origin of the flora of the Chihuahuan Desert in SW North America migrating to occupy North American arid lands. Vicariance and the expansion of arid lands allowed divergence, migration and permanence of the lineages studied on the Mexican Plateau. Divergence occurred prior to the onset of aridification. The Mexican Plateau acted as a refuge for hard‐leaved lineages during the Miocene. Shifts in ecological niches of related species allowed them to colonize new areas with different temperatures and precipitation. Current distribution of lineages is the most limited.

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We suggest that pre-Pleistocene changes had an influence on the divergence of Lindleya populations. We also suggest that the ancestral area for Lindleya was the Chihuahuan Desert and that the uplift of the Trans-Mexican Volcanic Belt isolated the Tehuacán Valley populations. Genetic and demographic analyses as well as and ecological niche modeling indicate that populations of Lindleya experienced genetic bottlenecks and that they have expanded since the Last Glacial Maximum.

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