BACKGROUND AND AIMS:Genetic information is essential for understanding evolutionary processes across different temporal scales, particularly those occurring over contemporary or recent generations influenced by management, and for guiding conservation actions. These components are now explicitly incorporated into the Kunming-Montreal Global Biodiversity Framework (GBF), which emphasizes metrics such as effective population size (Ne) as key indicators for monitoring and management. However, the genetic context of partially clonal and economically important systems remains insufficiently explored. Agave karwinskii, a mezcal-producing species with a restricted distribution in southern Mexico that occurs along a gradient of management intensity dominated by clonal propagation, provides an excellent model for informing conservation strategies in these understudied systems. METHODS:We generated genomic data using RADseq and conducted population-level analyses following the framework proposed by Funk et al., (2012), integrating the species' biological and management context to understand its genetics patterns and delineate conservation units. We additionally evaluated GBF-relevant indicators to assess genetic diversity and support management planning. KEY RESULTS:Agave karwinskii exhibited high genetic diversity (Hs = 0.25) and moderate population differentiation (FST = 0.19), shaped by geographical, ecological, and particularly by management factors. We identified 173 SNPs as candidate loci potentially associated with local adaptation to environmental variation, including 15 robust SNPs consistently detected by four complementary approaches and associated with defence responses, adaptation to environmental stressors, growth, and metabolic regulation. Two Evolutionarily Significant Units and seven Management Units were delineated. Ne declined sharply in clonal and semi-cultivated systems, with most units falling below the GBF threshold (Ne > 500), despite large census sizes. Traditional mixed management helps maintain diversity by promoting gene flow and reducing inbreeding, acting as a form of in situ conservation. CONCLUSIONS:This study provides a population genetic framework for understanding evolutionary processes influenced by management and guiding conservation strategies in A. karwinskii, offering insights applicable to other perennial, partially clonal, and semi-domesticated plant species.

The study of genomic diversity in domesticated species provides insights into their evolution and mechanisms of local adaptation, which are essential for conservation under climate change. Cucurbita moschata is a crop that is grown worldwide, with high landrace diversity in Mexico. Although previous studies have primarily focused on commercial varieties, landraces represent a valuable genetic reservoir. In this study we aimed to characterize the genomic diversity and structure of C. moschata, identify loci associated with environmental variables, and evaluate the best speciation model within the Argyrosperma group species. We analysed landraces from 24 Mexican localities, using nuclear Single Nucleotide Polymorphism (SNP) data. We assessed genetic structure through clustering analyses, performed an environmental association analysis, identified candidate loci potentially under selection, and inferred the evolutionary history with Approximate Bayesian Computation (ABC). Our results revealed that C. moschata has notable genetic variation (HT = 0.213) with low inbreeding signals (FIS = 0.0265). We identified two major landrace groups: one in the Yucatan Peninsula and another in the rest of Mexico. Furthermore, we found ecological structure, with landraces clustering according to arid and semi-arid conditions, vs. tropical regions. Outlier-based analyses revealed candidate loci related to abiotic stress responses, offering hypotheses for future studies on the adaptive potential of C. moschata landraces.

Social Impact Statement For hundreds of years, Agave marmorata plants have been used in the production of alcoholic beverages in Mexico. This species is very important in small‐scale rural economies because it is a large plant, yielding five liters of mezcal. However, the production of these beverages takes place when it reaches its reproductive stage, which takes up to 35 years. Due to its slow maturation and high demand, it is considered an endangered species. Therefore, as a conservation strategy, this study proposes the creation of nurseries, genetic breeding programs, and demographic monitoring of wild populations to counteract the extraction of wild plants and, the conservation of the genetic diversity. Summary Agave marmorata Roezl., is an endemic species distributed in the states of Oaxaca and Puebla, Mexico, and locally is widely used to produce mezcal. We assessed the genomic diversity and differentiation using the RADseq method and 29,101 high‐quality single nucleotide polymorphisms (SNPs) in wild plants and grown under three different management types (cultivated, plants used as live fences, and young plants growing in nurseries). We examined the demographic history and used species distribution modeling to understand the future of A. marmorata under scenarios of climate change. We found high levels of genomic diversity (H S = 0.229) and moderate levels of inbreeding (F IS = 0.106 and Fhat3 = 0.190). The cultivated samples harbored less genetic diversity than the wild plants. Furthermore, we estimated low differentiation between cultivated and wild localities (F ST = 0.037). In the wild samples, we identified two main genetic groups, one in the East and another in the West of its distribution area. This genetic structure possibly derived from a population contraction during the Pleistocene (~216,879.75 BP) and the formation of two refugia in small areas with climatic stability. Furthermore, the demographic reconstruction indicated that A. marmorata went through a recent population expansion event, with a large current N e ( N e = 8,009). The future climate change models indicated contrasting possible changes in its distribution range, from an increase to the reduction of its suitable habitat, differences related to model parametrization, and future levels of CO 2 production. We propose conservation measures for the different management types of the species while also considering the biotic and abiotic interactions of Agave marmorata .

Background and aims – Endemism may be defined according to the time of origin of taxa. Neo-endemics refer to relatively recent species that have not dispersed outside their ancestral areas. In contrast, paleo-endemics refer to species of ancient origins, which are currently geographically restricted but probably were more widespread in the past. Geographically, endemism areas may also be based on the co-occurrence of more than one species. We aimed to qualitatively identify the neo-endemism and paleo-endemism of endemic Cactaceae of the Tehuacán-Cuicatlán Valley, as well as to quantitatively assess paleo- and neo-endemics areas. Material and methods – Using a dated molecular phylogeny of endemic Cactaceae, we defined paleo- and neo-endemics using an arbitrary boundary of 2.6 million years ago; we also assessed the significance of concentrations of these species using a categorical analysis of paleo- and neo-endemism. Key results – Our results showed that most endemic Cactaceae in the Tehuacán-Cuicatlán Valley arose throughout the Pleistocene, while categorical analysis indicated localised mixed- and super-endemism (including both paleo- and neo-endemics) areas. Conclusion – We suggest that paleo- and neo-endemics, as well as localised mixed-endemism areas, may have originated due to a probable high climatic stability in the Tehuacán-Cuicatlán Valley, which in addition to topographically rugged and ecologically complex zones (e.g. ecotones, isolated habitat patches) may have allowed it to function as a refuge throughout Pleistocene climatic changes, mainly promoting the speciation of neo-endemics, as well as the persistence of relatively few paleo-endemics.

Social Impact StatementThe genetic variation of crop wild relatives will be key for our survival, as environmental change represents an increasing global threat for agriculture and food security. Cucurbita lundelliana and Cucurbita okeechobeensis subsp. martinezii are wild relatives of cultivated squashes and pumpkins that could be used for crop improvement. A genomic approach was used to characterize genetic resources in these taxa, that is, to identify candidate sites in the genome involved in responses to abiotic stress, and to understand the roles of gene flow and environmental differentiation in their divergence. This study highlights the importance of conserving these two species as phytogenetic resources for crop improvement.Summary Crop wild relatives (CWR) are reservoirs of genetic diversity and they are important for the maintenance of crop evolutionary potential. Mexico is the centre of domestication and diversity for many CWR. The genus Cucurbita originated in America, where at least six independent domestication events took place. Nonetheless, Cucurbita CWR have been seldom studied. In the present study, we test the role of incomplete lineage sorting (ILS) and secondary contact in the divergence of C. okeechobeensis subsp. martinezii and C. lundelliana. Additionally, we seek to understand the role of environmental differentiation in their divergence. We obtained 1,638 single nucleotide polymorphisms (SNPs) for 107 individuals from the most recently diverged wild species in this genus, encompassing 25 localities of C. lundelliana and nine localities of C. okeechobeensis subsp. martinezii in Mexico. We found higher genetic variation in C. lundelliana (HE = 0.227) than in C. okeechobeensis subsp. martinezii (HE = 0.187). Each taxon constitutes a well‐differentiated genetic group, with an area of introgression in Pantanos de Centla. We found candidate loci associated to hydric and thermal stress, which could be valuable for crop improvement. Our study supported a scenario of ILS followed by secondary contact, where divergence was probably driven by Pleistocene climate change. These CWR represent important phytogenetic resources for crop improvement given their high levels of genetic variation and differentiation and their SNPs associated to different climatic variables.

Protected areas are of paramount relevance to conserving wildlife and ecosystem contributions to people. Yet, their conservation success is increasingly threatened by human activities including habitat loss, climate change, pollution, and species overexploitation. Thus, understanding the underlying and proximate drivers of anthropogenic threats is urgently needed to improve protected areas' effectiveness, especially in the biodiversity-rich tropics. We addressed this issue by analyzing expert-provided data on long-term biodiversity change (last three decades) over 14 biosphere reserves from the Mesoamerican Biodiversity Hotspot. Using multivariate analyses and structural equation modeling, we tested the influence of major socioeconomic drivers (demographic, economic, and political factors), spatial indicators of human activities (agriculture expansion and road extension), and forest landscape modifications (forest loss and isolation) as drivers of biodiversity change. We uncovered a significant proliferation of disturbance-tolerant guilds and the loss or decline of disturbance-sensitive guilds within reserves causing a "winner and loser" species replacement over time. Guild change was directly related to forest spatial changes promoted by the expansion of agriculture and roads within reserves. High human population density and low nonfarming occupation were identified as the main underlying drivers of biodiversity change. Our findings suggest that to mitigate anthropogenic threats to biodiversity within biosphere reserves, fostering human population well-being via sustainable, nonfarming livelihood opportunities around reserves is imperative.

The genetic diversity found in natural populations is the result of the evolutionary forces in response to historical and contemporary factors. The environmental characteristics and geological history of Mexico promoted the evolution and diversification of plant species, including wild relatives of crops such as the wild pumpkins (Cucurbita). Wild pumpkin species are found in a variety of habitats, evidencing their capability to adapt to different environments. Despite the potential value of wild Cucurbita as a genetic reservoir for crops, there is a lack of studies on their genetic diversity. Cucurbita radicans is an endangered species threatened by habitat destruction leading to low densities in small and isolated populations. Here, we analyze Genotype by Sequencing genomic data of the wild pumpkin C. radicans to evaluate the influence of factors like isolation, demographic history, and the environment shaping the amount and distribution of its genetic variation. We analyzed 91 individuals from 14 localities along its reported distribution. We obtained 5,107 SNPs and found medium-high levels of genetic diversity and genetic structure distributed in four main geographic areas with different environmental conditions. Moreover, we found signals of demographic growth related to historical climatic shifts. Outlier loci analysis showed significant association with the environment, principally with precipitation variables. Also, the outlier loci displayed differential changes in their frequencies in response to future global climate change scenarios. Using the results of genetic structure, outlier loci and multivariate analyses of the environmental conditions, we propose priority localities for conservation that encompass most of the genetic diversity of C. radicans.

The central Oaxaca Basin has a century-long history of agave cultivation and is hypothesized to be the region of origin of other cultivated crops. Widely cultivated for mezcal production, the perennial crop known as "espadín" is putatively derived from wild Agave angustifolia. Nevertheless, little is known about its genetic relationship to the wild A. angustifolia or how the decades-long clonal propagation has affected its genetics.Using restriction-site-associated DNA sequencing and over 8000 single-nucleotide polymorphisms, we studied aspects of the population genomics of wild and cultivated A. angustifolia in Puebla and Oaxaca, Mexico. We assessed patterns of genetic diversity, inbreeding, distribution of genetic variation, and differentiation among and within wild populations and plantations.Genetic differentiation between wild and cultivated plants was strong, and both gene pools harbored multiple unique alleles. Nevertheless, we found several cultivated individuals with high genetic affinity with wild samples. Higher heterozygosity was observed in the cultivated individuals, while in total, they harbored considerably fewer alleles and presented higher linkage disequilibrium compared to the wild plants. Independently of geographic distance among sampled plantations, the genetic relatedness of the cultivated plants was high, suggesting a common origin and prevalent role of clonal propagation.The considerable heterozygosity found in espadín is contained within a network of highly related individuals, displaying high linkage disequilibrium generated by decades of clonal propagation and possibly by the accumulation of somatic mutations. Wild A. angustifolia, on the other hand, represents a significant genetic diversity reservoir that should be carefully studied and conserved.

Phytochemical bio-guided studies are used to find compounds with biological activity. Flavonoids from seeds of Leucaenaspecies have antimicrobial activity in strains of medical interest, therefore, fresh seeds were collected from the town of Tlayacapan, Morelos, Mexico. The methanolic extracts were obtained by the maceration technique, targeted fractionation was performed using adsorption and molecular exclusion chromatographic techniques; to observe the antimicrobial activity, agardiffusion techniques were used; spectrometric and spectroscopic techniques were used for the characterization of D-pinitol, resulting from the fractionation of L. leucocephala. Antimicrobial activity was found on strains of Escherichia coliCUSI and Staphylococcus aureusATCC 29213 of the most polar fractions, identifying the responsible compounds by HPLC: caffeic acid, gallic acid, p-coumaric acid, quercetin, catechin and apigenin, these compounds can inhibit the activation enzymatic, synthesis of nucleicacids and proteins, chelating with different ions, etc.

Cedrela odorata is a native tree of economic importance, as its wood is highly demanded in the international market. In this work, the current and future distributions of C. odorata in Mexico under climate change scenarios were analyzed according to their optimal temperature ranges for seed germination. For the present distribution, 256 localities of the species' presence were obtained from the Global Biodiversity Information Facility (GBIF) database and modelled with MaxEnt. For the potential distribution, the National Center for Atmospheric Research model (CCSM4) was used under conservative and drastic scenarios (RCP2.6 and RCP8.5 Watts/m2, respectively) for the intermediate future (2050) and far future (2070). Potential distribution models were built from occurrence data within the optimum germination temperature range of the species. The potential distribution expanded by 5 and 7.8% in the intermediate and far future, respectively, compared with the current distribution. With the increase in temperature, adequate environmental conditions for the species distribution should be met in the central Mexican state of Guanajuato. The states of Chihuahua, Mexico, Morelos, Guerrero, and Durango presented a negative trend in potential distribution. Additionally, in the far future, the state of Chihuahua it is likely to not have adequate conditions for the presence of the species. For the prediction of the models, the precipitation variable during the driest month presented the greatest contribution. When the humidity is not limiting, the thermal climatic variables are the most important ones. Models based on its thermal niche for seed germination allowed for the identification of areas where temperature will positively affect seed germination, which will help maximize the establishment of plant populations and adaptation to different climate change scenarios.

PREMISE:Domestication of plant species results in phenotypic modifications and changes in biotic interactions. Most studies have compared antagonistic plant-herbivore interactions of domesticated plants and their wild relatives, but little attention has been given to how domestication influences plant-pollinator interactions. Floral attributes and interactions of floral visitors were compared between sister taxa of the genus Cucurbita (Cucurbitaceae), the domesticated C. moschata, C. argyrosperma ssp. argyrosperma and its wild progenitor C. argyrosperma ssp. sororia in the place of origin.METHODS:We conducted univariate and multivariate analyses to compare floral morphological traits and analyzed floral reward (nectar and pollen) quantity and quality between flowers of wild and domesticated Cucurbita taxa. Staminate and pistillate flowers of all three taxa were video recorded, and visitation and behavior of floral visitors were registered and analyzed.RESULTS:Most floral morphological characteristics of flowers of domesticated taxa were larger in both staminate and pistillate flowers. Staminate and pistillate flowers presented distinct correlations between floral traits and integration indices between domesticated and wild species. Additionally, pollen quantity and protein to lipid ratio were greater in domesticated species. Cucurbit pollen specialists, Eucera spp., had the highest probability of visit for all Cucurbita taxa.CONCLUSIONS:We provide evidence that floral traits of domesticated and wild Cucurbita species experienced different selection pressures. Domesticated Cucurbita species may have more resources invested towards floral traits, thereby increasing attractiveness to pollinators and potentially plant reproductive success. Wild ancestor plant populations should be conserved in their centers of origin to preserve plant-pollinator interactions.

A substantially rich diversity of the world's recorded useful plants (UPs) is captured within the Millennium Seed Bank collection hosted by the Royal Botanic Gardens, Kew, at Wakehurst, UK with 13,598 species (34%) belonging to 3696 genera and 325 families. This constitutes just over half of the total accessions and one third of the species and covers all 9 continents, 8 realms, 14 biomes, 34 biodiversity hotspots and 175 countries. The most common beneficial use category within the captured diversity is medicinal, then species with environmental, material, and human food value. About 86% of conserved UP species have a 'Least Concern' conservation status but 8% are identified as globally threatened. The advantages of mutual, continued, and long-term partnership (e.g., Mexico) are showcased when conserving plants important for local communities and addressing conservation challenges beyond seed banking. However, the geographic coverage suffers from a lack of partnerships with some parts of the world. Also, a low number of accessions contributed from many countries means that insufficient native range is yet to be captured for many species. This is particularly the case for restricted or narrow distribution species from families or genera with a high incidence of recalcitrant or short-lived seeds. Future planning must tailor better to cover the spatial distribution patterns for individual species, thereby improving the number of accessions and geographical coverage for those captured. Moreover, seed biology research should characterise desiccation tolerance and develop complementary, novel conservation methods, such as cryopreservation, to strengthen conservation options for UP species.

Agave potatorum Zucc. locally known as Tobalá, is an important species for mezcal production. It is a perennial species that takes 10 to 15 years to reach reproductive age. Because of high demand of Tobalá mezcal and the slow maturation of the plants, its wild populations have been under intense anthropogenic pressure. The main objective of this study was to estimate the genome-wide diversity in A. potatorum and determine if the type of management has had any effect on its diversity, inbreeding and structure. We analyzed 174 individuals (105 wild, 42 cultivated and 27 from nurseries) from 34 sites with a reduced representation genomic method (ddRADseq), using 14,875 SNPs. The diversity measured as expected heterozygosity was higher in the nursery and wild plants than in cultivated samples. We did not find private alleles in the cultivated and nursery plants, which indicates that the individuals under management recently derived from wild populations, which was supported by higher gene flow estimated from wild populations to the managed plants. We found low but positive levels of inbreeding (FIS = 0.082), probably related to isolation of the populations. We detected low genetic differentiation among populations (FST = 0.0796), with positive and significant isolation by distance. The population genetic structure in the species seems to be related to elevation and ecology, with higher gene flow among populations in less fragmented areas. We detected an outlier locus related to the recognition of pollen, which is also relevant to self-incompatibility protein (SI). Due to seed harvest and long generation time, the loss of diversity in A. potatorum has been gradual and artificial selection and incipient management have not yet caused drastic differences between cultivated and wild plants. Also, we described an agroecological alternative to the uncontrolled extraction of wild individuals.

Phytochemical bio-guided studies are used to find compounds with biological activity. Flavonoids from seeds of Leucaena species have antimicrobial activity in strains of medical interest, therefore, fresh seeds were collected from the town of Tlayacapan, Morelos, Mexico. The methanolic extracts were obtained by the maceration technique, targeted fractionation was performed using adsorption and molecular exclusion chromatographic techniques; to observe the antimicrobial activity, agar diffusion techniques were used; spectrometric and spectroscopic techniques were used for the characterization of D-pinitol, resulting from the fractionation of L. leucocephala. Antimicrobial activity was found on strains of Escherichia coli CUSI and Staphylococcus aureus ATCC 29213 of the most polar fractions, identifying the responsible compounds by HPLC: caffeic acid, gallic acid, p-coumaric acid, quercetin, catechin and apigenin, these compounds can inhibit the activation enzymatic, synthesis of nucleic acids and proteins, chelating with different ions, etc.

Cucurbita ficifolia is a squash grown from Mexico to Bolivia. Its ancestor is unknown, but it has limited compatibility with wild xerophytic Cucurbita from Mexico’s highlands. We assembled the reference genome of C. ficifolia and assessed the genetic diversity and historical demography of the crop in Mexico with 2524 nuclear single nucleotide polymorphisms (SNPs). We also evaluated the gene flow between C. ficifolia and xerophytic taxa with 6292 nuclear and 440 plastome SNPs from 142 individuals sampled in 58 sites across their area of sympatry. Demographic modelling of C. ficifolia supports an eight-fold decrease in effective population size at about 2409 generations ago (95% CI = 464–12,393), whereas plastome SNPs support the expansion of maternal lineages ca. 1906–3635 years ago. Our results suggest a recent spread of C. ficifolia in Mexico, with high genetic diversity (π = 0.225, FST = 0.074) and inbreeding (FIS = 0.233). Coalescent models suggest low rates of gene flow with C. radicans and C. pedatifolia, whereas ABBA-BABA tests did not detect significant gene flow with wild taxa. Despite the ecogeographic proximity of C. ficifolia and its relatives, this crop persists as a highly isolated lineage of puzzling origin.

Twenty-one years have elapsed of the 21st Century and within the framework of the celebration of the 100th volume of Botanical Sciences, it is relevant to assess the progress of the research on conservation and on the activities undertaken for protecting the plants of Mexico, including the complementary in situ and ex situ approaches. By means of a systematic search of scientific articles related to the conservation of the Mexican flora on the Web of Science database, for the 2000–2021 period, we identified different scientific inputs, all showing specific objectives for undertaking conservation activities. The publications that resulted from this search were classified into six categories: (a) Regions and Ecoregions; (b) Communities or Ecosystems; (c) Taxonomic Groups; (d) Species and Populations; (e) Botanical Gardens; and (f) Seed Banks. For these categories, the results are presented under the headings “in situ conservation” and “ex situ conservation.” Additionally, we assessed by a random examination, the bibliography used to support touristic development projects. The results show that, despite the wide temporal range considered in this review, and even though there is a vast number of publications related to the characterization of the Mexican biodiversity, the production of scientific work oriented to the development of plant conservation strategies and activities is still scarce. Also evident is the lack of connection and communication among researchers of different disciplines, highlighting the disciplinary or multidisciplinary activities that they undertake. Finally, ten conclusions are presented, and some future research activities are suggested for conserving the Mexican flora.

We apply an environmental domains approach to identify environmentally heterogeneous characteristics defining a landscape matrix. We built environmental layers for national, regional, and local scales, considering the different scales studies can have. We used a numerical classification of explicit spatial layers and performed a multivariate classification. Based on the domains obtained, we mapped the landscape's climatic heterogeneity and identified a comprehensive set of environmental variables that defined the landscape matrix at each scale. We specifically tested our approach for its suitability to define a sampling strategy for a landscape genetics study, using as focal species the rodent Heteromys pictus. Namely, from the domains obtained at the local scale, we selected sampling localities that comprised the broadest habitat heterogeneity, which we corroborated in the field. The landscape matrix thus generated was used with genetic data previously obtained for H. pictus. Our approach allowed identification of environmental variables significantly associated with dispersal (gene flow) of H. pictus individuals in their natural habitat. We demonstrate its adequacy to efficiently determine sampling localities -or landscape sites- that encompass the highest environmental heterogeneity, in explored and unexplored landscapes, enabling rapid identification of localities and their environmental characteristics where in situ information is scarce.

Mexico is home to 40% of the pine species in the world. By the year 2050, 20% of the Mexican forests could be lost because of climate change and other human-related activities. In this paper, we determine the potential areas for seed collecting of four species of the genus Pinus and its ex situ economic value under different future Climate Change Scenarios (CCS). The species analyzed were Pinus oocarpa Schiede ex Schltdl, P. rudis Endl., P. culminícola Andresen et Beaman and P. leiophylla Schiede ex Schltdl. and Cham which together accounts for 19% of the timber production in Mexico. Potential areas of distribution of populations in habitats with Annual Mean Maximum Temperatures (AMMT) for seed collection were modelled through a Geographic Information System and climate database. The seed storage economic value was determined by using the Collection Cost Method. The AMMT of P. oocarpa, P. rudis, P. culminícola and P. leiophylla were 28 °C, 20 °C, 18.3 °C and 27.4 °C, respectively. The economic losses from shortages of these species due to CCS in 2050, were estimated of 88.5 million (USD) and 67.16 million (USD) with severe and conservative future CCS, respectively. The nominal investment rate would be 8.84% or more, for storing seeds of the four species and withstanding climate change. An ex situ seed bank is a medium and long-term investment; among its benefits are establishing a market price for the use and conservation of species in the face of possible adverse scenarios.