The three oak species have formed a complex hybrid zone that is geographically structured as a mosaic, and comprising a wide range of genotypes, including hybrids between different species pairs, backcrosses and probable triple hybrids.

† Background and Aims The Tehuacán Valley in Mexico is a principal area of plant domestication in Mesoamerica. There, artificial selection is currently practised on nearly 120 native plant species with coexisting wild, silvicultural and cultivated populations, providing an excellent setting for studying ongoing mechanisms of evolution under domestication. One of these species is the columnar cactus Stenocereus pruinosus, in which we studied how artificial selection is operating through traditional management and whether it has determined morphological and genetic divergence between wild and managed populations. † Methods Semi-structured interviews were conducted with 83 households of three villages to investigate motives and mechanisms of artificial selection. Management effects were studied by comparing variation patterns of 14 morphological characters and population genetics (four microsatellite loci) of 264 plants from nine wild, silvicultural and cultivated populations. † Key Results Variation in fruit characters was recognized by most people, and was the principal target of artificial selection directed to favour larger and sweeter fruits with thinner or thicker peel, fewer spines and pulp colours others than red. Artificial selection operates in agroforestry systems favouring abundance (through not felling plants and planting branches) of the preferred phenotypes, and acts more intensely in household gardens. Significant morphological divergence between wild and managed populations was observed in fruit characters and plant vigour. On average, genetic diversity in silvicultural populations (H E ¼ 0 . 743) was higher than in wild (H E ¼ 0 . 726) and cultivated (H E ¼ 0 . 700) populations. Most of the genetic variation (90 . 58 %) occurred within populations. High gene flow (Nm FST . 2) was identified among almost all populations studied, but was slightly limited by mountains among wild populations, and by artificial selection among wild and managed populations. † Conclusions Traditional management of S. pruinosus involves artificial selection, which, despite the high levels of gene flow, has promoted morphological divergence and moderate genetic structure between wild and managed populations, while conserving genetic diversity.

Reduced water availability during drought can create major stress for many plant species. Within a species, populations with a history of seasonal drought may have evolved the ability to tolerate drought more than those in areas of high precipitation and low seasonality. In this study, we assessed response to water stress in a California oak species, Quercus lobata Née, by measuring changes in gene expression profiles before and after a simulated drought stress treatment through water deprivation of seedlings in a greenhouse setting. Using whole-transcriptome sequencing from nine samples from three collection localities, we identified which genes are involved in response to drought stress and tested the hypothesis that seedlings sampled from climatically different regions of the species range respond to water stress differently. We observed a surprisingly massive transcriptional response to drought: 35,347 of 68,434 contigs (52%) were differentially expressed before versus after drought treatment, of which 18,111 were down-regulated and 17,236 were up-regulated. Genes functionally associated with abiotic stresses and death were enriched among the up-regulated genes, whereas metabolic and cell part-related genes were enriched among the down-regulated. We found 56 contigs that exhibited significantly different expression responses to the drought treatment among the three populations (treatment × population interaction), suggesting that those genes may be involved in local adaptation to drought stress. These genes have stress response (e.g., WRKY DNA-binding protein 51 and HSP20-like chaperones superfamily protein), metabolic (e.g., phosphoglycerate kinase and protein kinase superfamily protein), transport/transfer (e.g., cationic amino acid transporter 7 and K+ transporter) and regulatory functions (e.g., WRKY51 and Homeodomain-like transcriptional regulator). Baseline expression levels of 1310 unique contigs also differed among pairs of populations, and they were enriched for metabolic and cell part-related genes. Out of the large fraction of the transcriptome that was differentially expressed in response to our drought treatment, we identified several novel genes that are candidates for involvement in local adaptation to drought.

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Oaxaca state is one of the main hotspots of biodiversity in Mexico, containing almost 40% of the Mexican vascular flora, due to its high variability in habitat and climatic conditions coupled with high elevations in mountains and low elevations in valleys. We studied the genetic diversity and population structure of Quercus candicans, Quercus crassifolia, and Quercus castanea across their geographical distribution in Oaxaca state to understand how the heterogeneous physiography had driven the genetic diversity and population differentiation in these three oak species. We found high levels of genetic diversity but ca. 40% of the populations had significant values of Wright's inbreeding coefficient. The analysis of molecular variance indicated that most of the variation occurred within populations in the three oak species. Resistance analyses showed connectivity among almost all the populations but barrier analysis found genetic breaks that limited gene flow among some populations of the oak species. Even in a heterogeneous environment such as in Oaxaca state, the oak species still have high levels of genetic diversity and landscape connectivity. However, it is necessary to maintain the genetic connectivity through the preservation of natural corridors with forests in good condition, which is necessary to maintain the cohesiveness of the species in the long term. It is also important to protect the centers of species diversity in Oaxaca state located in the subprovinces of Western Oaxacan Mountains and Valleys, Sierra Madre de Oaxaca, and Sierra Madre del Sur because they harbor most of the population genetic diversity and oak species richness, as has been shown in previous studies.

The Mexican highlands are areas of high biological complexity where taxa of Nearctic and Neotropical origin and different population histories are found. To gain a more detailed view of the evolution of the biota in these regions, it is necessary to evaluate the effects of historical tectonic and climate events on species. Here, we analyzed the phylogeographic structure, historical demographic processes, and the contemporary period, Last Glacial Maximum (LGM) and Last Interglacial (LIG) ecological niche models of Quercus castanea, to infer the historical population dynamics of this oak distributed in the Mexican highlands. A total of 36 populations of Q. castanea were genotyped with seven chloroplast microsatellite loci in four recognized biogeographic provinces of Mexico: the Sierra Madre Occidental (western mountain range), the Central Plateau, the Trans‐Mexican Volcanic Belt (TMVB, mountain range crossing central Mexico from west to east) and the Sierra Madre del Sur (SMS, southern mountain range). We obtained standard statistics of genetic diversity and structure and tested for signals of historical demographic expansions. A total of 90 haplotypes were identified, and 29 of these haplotypes were restricted to single populations. The within‐population genetic diversity was high (mean hS = 0.72), and among‐population genetic differentiation showed a strong phylogeographic structure (NST = 0.630 > GST = 0.266; p < .001). Signals of demographic expansion were identified in the TMVB and the SMS. The ecological niche models suggested a considerable percentage of stable distribution area for the species during the LGM and connectivity between the TMVB and the SMS. High genetic diversity, strong phylogeographic structure, and ecological niche models suggest in situ permanence of Q. castanea populations with large effective population sizes. The complex geological and climatic histories of the TMVB help to explain the origin and maintenance of a large proportion of the genetic diversity in this oak species.

We used mitochondrial DNA (mtDNA) sequence data and allele frequencies at eight microsatellite loci to examine the population genetic structure, estimate the divergence times of distinct lineages, and infer patterns associated with host colonization in populations of the bark beetle Dendroctonus approximatus in Mexico. Two haplotype groups were identified using mtDNA sequences in 71 individuals from 15 populations. The first group was distributed in the Sierra Madre Occidental (SMOc, Western Mexico), with some populations in the Faja Volcánica Transmexicana (Central Mexico), and the second was found in the Sierra Madre Oriental (SMOr, Eastern Mexico), with populations in the Sierra Madre del Sur (Southern Mexico). The estimated split between groups occurred in the late Pleistocene, around 0.195 Mya. Microsatellite allele frequencies revealed high genetic differentiation between pairwise populations, and genetic differentiation values indicated a genetic structure of isolation by distance. Both mtDNA sequence data and microsatellite allele frequencies indicated that D. approximatus had two independent colonization routes in Mexico, one through the SMOc and another along the SMOr. The widespread geographic distribution of D. approximatus in Mexico follows a model of population range expansion of two haplotype groups in which gene flow is restricted by the geographic separation between hosts imposed by physical barriers between populations.

Laelia speciosa is an orchid species listed as threatened of extinction in the Mexican standard NOM-059. Wild populations of L. speciosa have been declining due to fragmentation of its habitat and massive extraction for trading in local markets in Mexico. In this study, we aimed to evaluate the evolutionary potential of L. speciosa within a fragmented landscape of ca. 4000 km 2 in the Cuitzeo basin, State of Michoacán. We sampled 15 populations throughout the Cuitzeo basin and amplified eight nuclear microsatellite markers to assess genetic diversity, structure, and connectivity and to test for evidence of recent bottlenecks. Surprisingly, L. speciosa populations showed high genetic diversity, with values ranging from moderate to high compared with those reported for other orchid species. Also, the analysis of molecular variance and R ST results indicated the existence of low genetic differentiation, favored by its cross pollination habit which facilitates the maintenance of gene flow and that have been observed in other orchid species. Wright's within-population inbreeding (F IS ) was positive in all cases, denoting a heterozygosity deficit, with moderate-to-high values. Fragmentation may also lead to inbreeding due to either increased self-fertilization or mating between related individuals within remnant fragments. The L. speciosa populations examined showed evidence suggesting that some populations had recently gone through a bottleneck. We also observed that all the L. speciosa populations had a moderate effective population size. The history of L. speciosa in the Cuitzeo basin suggests that both fragmented and non-fragmented populations may have been recently subject to moderate reductions in effective population size, large enough to affect their allelic diversity, F IS , but not their H E . Such reductions may have been caused by episodic environmental fluctuations or resulted from the recent founding of some of the populations. The effective population size can be used as an indicator of habitat quality, and this was confirmed for the L. speciosa populations, which have undergone a drastic decline due to environmental changes, habitat destruction, and illegal collection. The ultimate goals of conservation are to ensure the continuous survival of populations and maintain their evolutionary potential by preserving natural levels of genetic diversity. Great efforts should be made to preserve this species' extant populations and their habitats to prevent further population reductions and preserve its overall genetic basis. Collection of this orchid should be banned and robust legal protection measures should be enforced through local authorities.