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Genetic differentiations and phylogeographical patterns are controlled by the interplay between spatial isolation and gene flow. To assess the extent of gene flow across an oceanic barrier, we explored the effect of the separation of the peninsula of Baja California on the evolution of mainland and peninsular populations of the long-lived columnar cactus Stenocereus thurberi . We analyzed twelve populations throughout the OPC distribution range to assess genetic diversity and structure using chloroplast DNA sequences. Genetic diversity was higher ( H d = 0.81), and genetic structure was lower ( G ST = 0.143) in mainland populations vs peninsular populations ( H d = 0.71, G ST = 0.358 respectively). Genetic diversity was negatively associated with elevation but positively with rainfall. Two mainland and one peninsular ancestral haplotypes were reconstructed. Peninsular populations were as isolated among them as with mainland populations. Peninsular haplotypes formed a group with one mainland coastal population, and populations across the gulf shared common haplotypes giving support to regular gene flow across the Gulf. Gene flow is likely mediated by bats, the main pollinators and seed dispersers. Niche modeling suggests that during the Last Glacial Maximum (c. 130 ka), OPC populations shrank to southern locations. Currently, Stenocereus thurberi populations are expanding, and the species is under population divergence despite ongoing gene flow. Ancestral populations are located on the mainland and although vicariant peninsular populations cannot be ruled out, they are likely the result of gene flow across the seemingly formidable barrier of the Gulf of California. Still, unique haplotypes occur in the peninsula and the mainland, and peninsular populations are more structured than those on the mainland.

Bats are the main pollinators and seed dispersers of Stenocereus thurberi, a xenogamous columnar cactus of northwestern Mexico and a good model to illustrate spatial dynamics of gene flow in long-lived species. Previous studies in this cactus showed differences among populations in the type and abundance of pollinators, and in the timing of flowering and fruiting. In this study we analyzed genetic variability and population differentiation among populations. We used three primers of ISSR to analyze within and among populations genetic variation from eight widely separated populations of S. thurberi in Sonora, Mexico. Sixty-six out of 99 of the ISSR bands (P = 66.7%) were polymorphic. Total heterozygosity for all populations sampled revealed high genetic diversity (Hsp = 0.207, HBT = 0.224). The AMOVA showed that most of the genetic variation was within populations (80.5%). At the species level, estimates of population differentiation, θ = 0.175 and θB = 0.194, indicated moderate gene flow among populations. The absence of a significant correlation between genetic and geographic distances indicated little isolation by geographic distance. The large genetic variation and diversity found in S. thurberi is consistent with its open reproductive system and the high mobility of bats, a major pollinator. However, small changes in number or kind of pollinators and seed dispersal agents, in the directionality of migratory routes, and/or in the timing of flowering and fruiting among populations, can critically affect gene flow dynamics.

It is still an open question as to whether genome size (GS) variation is shaped by natural selection. One approach to address this question is a population-level survey that assesses both the variation in GS and the relationship of GS to ecological variants. We assessed GS in Zea mays, a species that includes the cultivated crop, maize, and its closest wild relatives, the teosintes. We measured GS in five plants of each of 22 maize landraces and 21 teosinte populations from Mexico sampled from parallel altitudinal gradients. GS was significantly smaller in landraces than in teosintes, but the largest component of GS variation was among landraces and among populations. In maize, GS correlated negatively with altitude; more generally, the best GS predictors were linked to geography. By contrast, GS variation in teosintes was best explained by temperature and precipitation. Overall, our results further document the size flexibility of the Zea genome, but also point to a drastic shift in patterns of GS variation since domestication. We argue that such patterns may reflect the indirect action of selection on GS, through a multiplicity of phenotypes and life-history traits.

The Tehuacán-Cuicatlán Valley, located at the southeast of the state of Puebla and the northeast of the state of Oaxaca in Central Mexico, south of the Trans-Mexican Volcanic Belt (TMVB), is of particular interest for understanding the evolutionary dynamics of arid and semi-arid environments, being one of the main reservoirs of biological diversity for the arid zones of North America, including the highest diversity of Agavaceae worldwide and high levels of endemism. Studying in detail the phylogeography, environmental history and population genetics of representative species will hopefully shed light on the evolutionary and ecological dynamics that generated the tremendous biodiversity and endemism of this important region in Mexico. We sequenced three non-coding regions of chloroplast genome of Agave kerchovei , a representative species of the Tehuacán Valley, generating 2,188 bp from 128 individuals sampled from eight populations throughout the species range. We used this data set to (i) characterize the levels of genetic diversity and genetic structure in A. kerchovei ; (ii) predict the distribution of A. kerchovei for the present day, and to reconstruct the past geographical history of the species by constructing ecological niche models (ENM); and (iii) compare the levels of diversity in this species with those estimated for the widely distributed Agave lechuguilla . Agave kerchovei has high levels of total chloroplast genetic variation ( Hd = 0.718), especially considering that it is a species with a very restricted distribution. However, intrapopulation diversity is low (zero in some populations), and genetic structure is high ( F ST = 0.928, G ST = 0.824), which can be expected for endemic species with isolated populations. Our data suggest that Pleistocene glacial cycles have played an important role in the distribution of A. kerchovei , where the climatic variability of the region – likely associated with its topographic complexity – had a significant effect on the levels of genetic diversity and population dynamics, while the potential distribution of the species seems to be stable since the middle Holocene (6 kya). We conclude that in A. kerchovei there is a core group of populations in the Tehuacán Valley, and peripheric populations that appear to be evolving independently and thus the species is fundamentally an endemic species from the Tehuacán Valley while the populations outside the Valley appear to be in the process of incipient speciation.

Background In bacteria, pan-genomes are the result of an evolutionary “tug of war” between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size ( N e ), resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced by HGT and mutation, resulting in closed pan-genomes and clonal lineages. In this study, we explored both hypotheses, elucidating the pan-genome of Vibrionaceae isolates after a perturbation event in the endangered oasis of Cuatro Ciénegas Basin (CCB), Mexico, and looking for signals of adaptation to the environments in their genomes. Results We obtained 42 genomes of Vibrionaceae distributed in six lineages, two of them did not showed any close reference strain in databases. Five of the lineages showed closed pan-genomes and were associated to either water or sediment environment; their high N e estimates suggest that these lineages are not from a recent origin. The only clade with an open pan-genome was found in both environments and was formed by ten genetic groups with low N e , suggesting a recent origin. The recombination and mutation estimators ( r/m ) ranged from 0.005 to 2.725, which are similar to oceanic Vibrionaceae estimations. However, we identified 367 gene families with signals of positive selection, most of them found in the core genome; suggesting that despite recombination, natural selection moves the Vibrionaceae CCB lineages to local adaptation, purging the genomes and keeping closed pan-genome patterns. Moreover, we identify 598 SNPs associated with an unstructured environment; some of the genes associated with these SNPs were related to sodium transport. Conclusions Different lines of evidence suggest that the sampled Vibrionaceae, are part of the rare biosphere usually living under famine conditions. Two of these lineages were reported for the first time. Most Vibrionaceae lineages of CCB are adapted to their micro-habitats rather than to the sampled environments. This pattern of adaptation is concordant with the association of closed pan-genomes and local adaptation.

For more than 20 years cotton has been the most widely sown genetically modified (GM) crop in Mexico. Its cultivation has fulfilled all requirements and has gone through the different regulatory stages. During the last 20 years, both research-institutions and biotech-companies have generated scientific and technical information regarding GM cotton cultivation in Mexico. In this work, we collected data in order to analyze the environmental and agronomic effects of the use of GM cotton in Mexico. In 1996, the introduction of Bt cotton made it possible to reactivate this crop, which in previous years was greatly reduced due to pest problems, production costs and environmental concerns. Bt cotton is a widely accepted tool for cotton producers and has proven to be efficient for the control of lepidopteran pests. The economic benefits of its use are variable, and depend on factors such as the international cotton-prices and other costs associated with its inputs. So far, the management strategies used to prevent development of insect resistance to GM cotton has been successful, and there are no reports of insect resistance development to Bt cotton in Mexico. In addition, no effects have been observed on non-target organisms. For herbicide tolerant cotton, the prevention of herbicide resistance has also been successful since unlike other countries, the onset of resistance weeds is still slow, apparently due to cultural practices and rotation of different herbicides. Environmental benefits have been achieved with a reduction in chemical insecticide applications and the subsequent decrease in primary pest populations, so that the inclusion of other technologies-e.g., use of non-Bt cotton- can be explored. Nevertheless, control measures need to be implemented during transport of the bolls and fiber to prevent dispersal of volunteer plants and subsequent gene flow to wild relatives distributed outside the GM cotton growing areas. It is still necessary to implement national research programs, so that biotechnology and plant breeding advances can be used in the development of cotton varieties adapted to the Mexican particular environmental conditions and to control insect pests of regional importance.

Social Impact Statement The 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. La variación genética de los parientes silvestres de los cultivos será clave para nuestra sobrevivencia, dado que el cambio ambiental representa una amenaza global creciente tanto para la agricultura como para la seguridad alimentaria. Cucurbita lundelliana y Cucurbita okeechobeensis subsp. martinezii son parientes silvestres de las calabazas cultivadas que pueden ser utilizadas para el mejoramiento de los cultivos. Una aproximación genómica fue utilizada para caracterizar los recursos genéticos de estos taxa, es decir, para identificar sitios candidatos en el genoma que pueden estar involucrados en la respuesta al estrés abiótico, y para comprender el papel de flujo génico y de la diferenciación ambiental en su divergencia. Este estudio resalta la importancia de conservar estas especies como recursos fitogenéticos para el mejoramiento de los cultivos. The 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.

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.

Aim: The history of Agave lechuguilla, a characteristic and dominant plant of the Chihuahuan Desert, was reconstructed in order to determine the importance of the Neogene orogenic uplift and the Quaternary glacial-interglacial climatic changes on the genetic patterns of a native Chihuahuan Desert species. Location: Chihuahuan Desert, Mexico and United States. Methods: Chloroplast DNA data from A. lechuguilla were analysed to describe levels of genetic diversity and structure and to infer the species' demographic history, using traditional methods and approximate Bayesian computation (ABC). The time of divergence of the different haplogroups was estimated with a Bayesian approach. In addition, ecological niche modelling was used to identify possible refugia. Results: Molecular dating analyses showed that A. lechuguilla originated 4.46 Ma and later differentiated into four haplogroups. The average chloroplast genetic diversity was low (Hd, 0.24), with high levels of genetic differentiation (GST, 0.780). Demographic analysis, niche modelling and ABC indicated a recent expansion from at least five glacial refugia located south of the species' current distribution. Main conclusion: Agave lechuguilla originated in the Neogene, and the glacial-interglacial events of the Pleistocene resulted in the expansion and contraction of its range, playing an important role in its intraspecific diversification. These contraction-expansion events are consistent with biogeographical regions previously identified in the Chihuahuan Desert.

• Premise of the study: Although species adapted to grow in unusual soils contribute importantly to regional diversity, the microevolutionary processes responsible for that diversity remain to be understood. We aimed to answer this question by analyzing which processes are responsible for the genetic differentiation in Fouquieria shrevei (Fouquieriaceae), a species confined to gypsum soils of northern Mexico.• Methods: We analyzed sequence variation in three chloroplast intergenic spacers from five populations.• Key results: Total genetic diversity was high (Hd = 0.743). Genetic differentiation was high (FST = 0.651), as most haplotypes were unique to individual populations, and three populations had only one haplotype. Haplotypes were more similar in nearby populations, resulting in a phylogeographic structure (i.e., GST = 0.850 was significantly lower than NST = 0.930) and a significant Mantel test (P = 0.04). Tajima’s D (−0.019, not significant) indicates that effective population size has remained constant.• Conclusions: We conclude that genetic drift has been intense and gene flow low in differentiating populations that follow an island-like pattern of gypsum deposits of the deserts of North America. The interaction between these forces could promote speciation events that in turn would increase regional diversity and may explain the high number of narrow endemics associated with soil restrictions.