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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 (HS = 0.229) and moderate levels of inbreeding (FIS = 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 (FST = 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 Ne (Ne = 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 CO2 production. We propose conservation measures for the different management types of the species while also considering the biotic and abiotic interactions of Agave marmorata.

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.

Abstract Agaves are an outstanding arid‐adapted group of species that provide a unique chance to study the influence of multiple potential factors (i.e., geological and ecological) on plant population structure and diversification in the heterogeneous environment of the Baja California Peninsula. However, relatively little is known about the phylogeography of the endemic agave species of this region. Herein, we used over 10,000 single‐nucleotide polymorphisms (SNPs) and spatial data from the Agave aurea species complex (i.e., A. aurea ssp. aurea, A. aurea ssp. promontorii, and A. aurea var. capensis) to resolve genetic relationships within this complex and uncover fine‐scale population structure, diversity patterns, and their potential underlying drivers. Analyses resolved low genetic structure within this complex, suggesting that A. aurea is more likely to represent several closely related populations than separate species or varieties/subspecies. We found that geographical and historical ecological characteristics—including precipitation, latitude, and past climatic fluctuations—have played an important role in the spatial distribution of diversity and structure in A. aurea. Finally, species distribution modeling results suggested that climate change will become critical in the extinction risk of A. aurea, with the northernmost population being particularly vulnerable. The low population genetic structure found in A. aurea is consistent with agave's life history, and it is probably related to continuity of distribution, relatively low habitat fragmentation, and dispersion by pollinators. Together, these findings have important implications for management and conservation programs in agave, such as creating and evaluating protected areas and translocating and augmentation of particular populations.

Background Genomic resource development for non-model organisms is rapidly progressing, seeking to uncover molecular mechanisms and evolutionary adaptations enabling thriving in diverse environments. Limited genomic data for bat species hinder insights into their evolutionary processes, particularly within the diverse Myotis genus of the Vespertilionidae family. In Mexico, 15 Myotis species exist, with three—M. vivesi, M. findleyi, and M. planiceps—being endemic and of conservation concern. Methods We obtained samples of Myotis vivesi, M. findleyi, and M. planiceps for genomic analysis. Each of three genomic DNA was extracted, sequenced, and assembled. The scaffolding was carried out utilizing the M. yumanensis genome via a genome-referenced approach within the ntJoin program. GapCloser was employed to fill gaps. Repeat elements were characterized, and gene prediction was done via ab initio and homology methods with MAKER pipeline. Functional annotation involved InterproScan, BLASTp, and KEGG. Non-coding RNAs were annotated with INFERNAL, and tRNAscan-SE. Orthologous genes were clustered using Orthofinder, and a phylogenomic tree was reconstructed using IQ-TREE. Results We present genome assemblies of these endemic species using Illumina NovaSeq 6000, each exceeding 2.0 Gb, with over 90% representing single-copy genes according to BUSCO analyses. Transposable elements, including LINEs and SINEs, constitute over 30% of each genome. Helitrons, consistent with Vespertilionids, were identified. Values around 20,000 genes from each of the three assemblies were derived from gene annotation and their correlation with specific functions. Comparative analysis of orthologs among eight Myotis species revealed 20,820 groups, with 4,789 being single copy orthogroups. Non-coding RNA elements were annotated. Phylogenomic tree analysis supported evolutionary chiropterans’ relationships. These resources contribute significantly to understanding gene evolution, diversification patterns, and aiding conservation efforts for these endangered bat species.

Modern microbial mats are relictual communities mostly found in extreme environments worldwide. Despite their significance as representatives of the ancestral Earth and their important roles in biogeochemical cycling, research on microbial mats has largely been localized, focusing on site-specific descriptions and environmental change experiments. Here, we present a global comparative analysis of non-lithifying microbial mats, integrating environmental measurements with metagenomic data from 62 samples across eight sites, including two new samples from the recently discovered Archaean Domes from Cuatro Ciénegas, Mexico. Our results revealed a notable influence of environmental filtering on both taxonomic and functional compositions of microbial mats. Functional redundancy appears to confer resilience to mats, with essential metabolic pathways conserved across diverse and highly contrasting habitats. We identified six highly correlated clusters of taxa performing similar ecological functions, suggesting niche partitioning and functional specialization as key mechanisms shaping community structure. Our findings provide insights into the ecological principles governing microbial mats, and lay the foundation for future research elucidating the intricate interplay between environmental factors and microbial community dynamics.

A comprehensive study was conducted in the Cuatro Ciénegas Basin (CCB) in Coahuila, Mexico, which is known for its diversity of microorganisms and unique physicochemical properties. The study focused on the “Archaean Domes” (AD) site in the CCB, which is characterized by an abundance of hypersaline, non-lithifying microbial mats. In AD, we analyzed the small domes and circular structures using metagenome assembly genomes (MAGs) with the aim of expanding our understanding of the prokaryotic tree of life by uncovering previously unreported lineages, as well as analyzing the diversity of bacteria and archaea in the CCB. A total of 325 MAGs were identified, including 48 Archaea and 277 Bacteria. Remarkably, 22 archaea and 104 bacteria could not be classified even at the genus level, highlighting the remarkable novel diversity of the CCB. Besides, AD site exhibited significant diversity at the phylum level, with Proteobacteria being the most abundant, followed by Desulfobacteria, Spirochaetes, Bacteroidetes, Nanoarchaeota, Halobacteriota, Cyanobacteria, Planctomycetota, Verrucomicrobiota, Actinomycetes and Chloroflexi. In Archaea, the monophyletic groups of MAGs belonged to the Archaeoglobi, Aenigmarchaeota, Candidate Nanoarchaeota, and Halobacteriota. Among Bacteria, monophyletic groups were also identified, including Spirochaetes, Proteobacteria, Planctomycetes, Actinobacteria, Verrucomicrobia, Bacteroidetes, Candidate Bipolaricaulota, Desulfobacteria, and Cyanobacteria. These monophyletic groups were possibly influenced by geographic isolation, as well as the extreme and fluctuating environmental conditions in the pond AD, such as stoichiometric imbalance of C:N:P of 122:42:1, fluctuating pH (5–9.8) and high salinity (5.28% to saturation).

The topographical, geological, climatic and biodiversity complexity of Mesoamerica has made it a primary research focus. The Mesoamerican highlands is a region with particularly high species richness and within-species variation. The Cinnamon-bellied Flowerpiercer, Diglossa baritula (Wagler, 1832), is a species endemic to the Mesoamerican highlands, with three allopatric subspecies currently recognized. To characterize divergence within this species, we integrated genomics, morphology, coloration and ecological niche modeling approaches, obtained from sampling individuals across the entire geographic distribution of the species. Our results revealed a clear genomic divergence between the populations to the east versus the west of the Isthmus of Tehuantepec. In contrast to the genomic results, morphology and coloration analyses showed intermediate levels of differentiation, indicating that population groups within D. baritula have probably been under similar selective pressures. Our morphology results indicated that the only sexually dimorphic morphological variable is the wing chord, with males having a longer wing chord than females. Finally, ecological data indicated that there are differences in ecological niche within D. baritula. Our data suggest that D. baritula could contain two or more incipient species at the intermediate phase of the speciation continuum. These results highlight the importance of the geographical barrier of the Isthmus of Tehuantepec and Pleistocene climatic events in driving isolation and population divergence in D. baritula. The present investigation illustrates the speciation potential of the D. baritula complex and the capacity of Mesoamerican highlands to create cryptic biodiversity and endemism.

Agrostis is one of the most diverse genera of the Poaceae, including ca. 198 species, principally distributed in cold and temperate regions of the world, but also found in the high mountains of the tropics. We present a revision based on morphoanatomical evidence, for the biogeographic region known as Megamexico 3 (i.e., Mexico including the desert areas of southern USA and the Central America territory, to northern Nicaragua). We include taxonomic descriptions and an identification key for the found taxa, maps with the known geographical distribution of the species, and figures with the morphoanatomical characteristics, elevation and phenology. Agrostis is represented in the study zone by 20 species, of which four are endemic and three are introduced. Most records of the genus are distributed in the mountains, above 1500 m a.s.l., in open areas of temperate forests, with conifers and Quercus. Specimens with spikelets occur year round, but most records occur during the wet season, in the months of July to October. We propose a preliminary conservation assessment for each species in the study zone, according to the International Union for Conservation of Nature categories: one with Deficient Data (DD), six as Endangered (EN), two as Vulnerable (VU), and 11 as Least Concern (LC).

Animal hosts live in continuous interaction with bacterial partners, yet we still lack a clear understanding of the ecological drivers of animal-associated bacteria, particularly in seabirds. Here, we investigated the effect of body site in the structure and diversity of bacterial communities of two seabirds in the Strait of Magellan: the Magellanic penguin (Spheniscus magellanicus) and the king penguin (Aptenodytes patagonicus). We used 16S rRNA gene sequencing to profile bacterial communities associated with body sites (chest, back, foot) of both penguins and the nest soil of Magellanic penguin. Taxonomic composition showed that Moraxellaceae family (specifically Psychrobacter) had the highest relative abundance across body sites in both penguin species, whereas Micrococacceae had the highest relative abundance in nest soil. We were able to detect a bacterial core among 90% of all samples, which consisted of Clostridium sensu stricto and Micrococcacea taxa. Further, the king penguin had its own bacterial core across its body sites, where Psychrobacter and Corynebacterium were the most prevalent taxa. Microbial alpha diversity across penguin body sites was similar in most comparisons, yet we found subtle differences between foot and chest body sites of king penguins. Body site microbiota composition differed across king penguin body sites, whereas it remained similar across Magellanic penguin body sites. Interestingly, all Magellanic penguin body site microbiota composition differed from nest soil microbiota. Finally, bacterial abundance in penguin body sites fit well under a neutral community model, particularly in the king penguin, highlighting the role of stochastic process and ecological drift in microbiota assembly of penguin body sites. Our results represent the first report of body site bacterial communities in seabirds specialized in subaquatic foraging. Thus, we believe it represents useful baseline information that could serve for long-term comparisons that use marine host microbiota to survey ocean health.

Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as “microbial gardening”. In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species in the Strait of Magellan. In the short-term, the project will improve our knowledge about microbial diversity in the region, while long-term potential benefits include the use of these data to assess host-microbial responses to the Anthropocene derived climate change.

Germination traits are components of invasion potential, and comparing seed traits in sympatric native and invasive species can offer insights into the invasion process. We characterized seed germination traits and how they influenced the success of Eragrostis mexicana, a native species, and Eragrostis tenuifolia, an exotic species (Poaceae) in Mexico, in the context of their potential for biological invasion. Seeds from both species were collected from four sites in a natural protected area in Mexico City, and the germination of seeds of different ages was conducted in experiments at different temperatures. E. tenuifolia exhibited higher germination percentages than the native E. mexicana across all treatments. Seed age had differential effects, with older seeds of the native E. mexicana germinating better, while E. tenuifolia performed better with younger seeds. Temperature positively impacted germination for both species, although E. mexicana was limited at lower temperatures. Exotic E. tenuifolia can germinate over a wider temperature range with earlier germination rates, and generate a seed bank lasting several years, which may contribute to naturalization. The importance of germination traits in the context of invasive species establishment underscores the potential role of seed banks in facilitating biological invasions.

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.

Background Genetic diversity is fundamental for the survival of species. In particular, in a climate change scenario, it is crucial that populations maintain genetic diversity so they can adapt to novel environmental conditions. Genetic diversity in wild agaves is usually high, with low genetic differentiation among populations, in part maintained by the agave pollinators such as the nectarivorous bats. In cultivated agaves, patterns of genetic diversity vary according to the intensity of use, management, and domestication stage. In Agave tequilana Weber var. azul (A. tequilana thereafter), the plant used for tequila production, clonal propagation has been strongly encouraged. These practices may lead to a reduction in genetic diversity. Methods We studied the diversity patterns with genome-wide SNPs, using restriction site associated DNA sequencing in cultivated samples of A. tequilana from three sites of Jalisco, Mexico. For one locality, seeds were collected and germinated in a greenhouse. We compared the genomic diversity, levels of inbreeding, genetic differentiation, and connectivity among studied sites and between adults and juvenile plants. Results Agave tequilana presented a genomic diversity of HT = 0.12. The observed heterozygosity was higher than the expected heterozygosity. Adults were more heterozygous than juveniles. This could be a consequence of heterosis or hybrid vigor. We found a shallow genetic structure (average paired FST = 0.0044). In the analysis of recent gene flow, we estimated an average migration rate among the different populations of m = 0.25. In particular, we found a population that was the primary source of gene flow and had greater genomic diversity (HE and HO), so we propose that this population should continue to be monitored as a potential genetic reservoir. Discussion Our results may be the consequence of more traditional management in the studied specific region of Jalisco. Also, the exchange of seeds or propagules by producers and the existence of gene flow due to occasional sexual reproduction may play an important role in maintaining diversity in A. tequilana. For populations to resist pests, to continue evolving and reduce their risk of extinction under a climate change scenario, it is necessary to maintain genetic diversity. Under this premise we encourage to continue acting in conservation programs for this species and its pollinators.

Abstract Climate changes, together with geographical barriers imposed by the Sierra Madre Oriental and the Chihuahuan Desert, have shaped the genetic diversity and spatial distribution of different species in northern Mexico. Pinus pinceana Gordon & Glend. tolerates extremely arid conditions. Northern Mexico became more arid during the Quaternary, modifying ecological communities. Here, we try to identify the processes underlying the demographic history of P. pinceana and characterize its genetic diversity using 3100 SNPs from genotyping by sequencing 90 adult individuals from 10 natural populations covering the species' entire geographic distribution. We inferred its population history and contrasted possible demographic scenarios of divergence that modeled the genetic diversity present in this restricted pinyon pine; in support, the past distribution was reconstructed using climate from the Last Glacial Maximum (LGM, 22 kya). We inferred that P. pinceana diverged into two lineages ~2.49 Ma (95% CI 3.28–1.62), colonizing two regions: the Sierra Madre Oriental (SMO) and the Chihuahuan Desert (ChD). Our results of population genomic analyses reveal the presence of heterozygous SNPs in all populations. In addition, low migration rates across regions are probably related to glacial–interglacial cycles, followed by the gradual aridification of the Chihuahuan Desert during the Holocene.

Plant genomes contain huge troves of information, and nowadays molecular tools to analyze genomes are less expensive and keep improving. In this review, we aimed to produce a “roadmap” to take advantage of this explosion of molecular methods and opportunities. We explain how to decide which strategies are adequate for a given evolutionary or taxonomic problem by describing 15 possible (and in some cases nonconsecutive) steps to take advantage of all the genomic resources drawing from the ever-increasing studies. We describe how to obtain an adequate genome sequence given our study species and objectives and discuss if we need to also obtain a transcriptome and additional “omic” data (i.e., proteome, metabolome, epigenome, microbiome). We analyze what is needed to conduct population genomics studies in terms of genomic methods and sampling strategies and discuss the pangenome concept. In addition, we present some considerations about how to estimate population genetics parameters and how to analyze geographic differentiation, inbreeding and gene flow. We examine ideas and methods on how to estimate natural selection and local adaptation, how to detect candidate genes, how coalescent analyses can help in these studies, the importance of genomic information for conservation studies and to understand adaptability to climate change. We assess the use of these methods in domestication studies and in understanding how form and function can be inferred from genes; likewise, how to use the genomic information for improvement of cultivated plants. We also review how can we use these methods in phylogenomic studies.

We evaluated the microbial diversity and metabolome profile of an uncommon hypersaline elastic microbial mat from Cuatro Ciénegas Basin (CCB) in the Chihuahuan Desert of Coahuila, México. We collected ten samples on a small scale transect (1.5-m) and described its microbial diversity through NGS-based ITS and 16S rDNA gene sequencing. A very low number of taxa comprised a considerable proportion of the mat and were shared across all sampling points, whereas the rare biosphere was more phylogenetically diverse (Faith’s Phylogenetic Diversity (FPD) index) and phylogenetically disperse (using a null model distribution of Phylogenetic Species Clustering (nmdPSC)) than the abundant (high read count) taxa for both analyzed libraries. We also found a distinctive metabolome profile for each sample and were able to tentatively annotate several classes of compounds with relevant biological properties.

Pozas Rojas is a hydrological system comprising nine isolated shallow ponds and a deep lagoon, which were temporally merged in 2010 by increased rainfall due to a tropical cyclone. In this work, we assess which components, biotic interactions, or environment filtering effects, drive the assembly of microbial communities after a natural perturbation. Arsenic, pH, and temperature are among the most significant environmental variables between each pond, clustering the samples in two main groups, whereas microbial composition is diverse and unique to each site, with no core at the operational taxonomic unit level and only 150 core genera when studied at the genus level. Los Hundidos lagoon has the most differentiated community, which is highly similar to the epipelagic Mediterranean Sea communities. On the other hand, the shallow ponds at the Pozas Rojas system resemble more to epicontinental hydrological systems, such as some cold rivers of the world and the phreatic mantle from Iowa. Overall, despite being a sole of water body 2 years prior to the sampling, interspecific interactions, rather than environmental selection, seem to play a more important role in Pozas Rojas, bolstered by founder effects on each poza and subsequent isolation of each water body.

Fungal ecological interactions play a key role in structuring community assemblages. These associations may involve both antagonistic and synergistic relationships, which are commonly influenced by abiotic factors such as nutrient conditions. However, information for extreme, oligotrophic systems remain poor. Herein, interactions among key members of the aquatic transient fungal community (Aspergillus niger, Cladosporium sp., and Coprinellus micaceus) of a low-nutrient freshwater system in the Cuatro Ciénegas Basin, Mexico were studied. Pairwise interaction bioassays were explored in vitro under different nutrient conditions, including carbohydrates-rich, carbohydrates and amino peptides-rich, and low nutrients. Our results indicated that antagonistic patterns prevail among the studied taxa. However, nutrient-dependent changes were observed in Cladosporium sp. shifting to synergy under carbohydrates-rich conditions, suggesting changes in the fungal community composition as a result of nutrient enrichment. Remarkably, our findings contrast with previous work demonstrating mainly synergistic interactions between our tested fungal isolates and co-occurring autochthonous bacteria (Aeromonas spp. and Vibrio sp.) under low-nutrient conditions. This observation may indicate that bacteria and fungi exhibit distinct community-level responses, driven by nutrient conditions. This contributes to the knowledge of fungal community dynamics and interspecific interactions in an oligotrophic ecosystem, highlighting the relevance of nutrient-based shifts and antagonistic interactions in ecosystem dynamics.

Abstract 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.

Abstract Background Most reports of domesticated plants that involve a domestication gradient or inter-specific hybridization in Mexico have focused on those used as food. This study provides knowledge about these processes in two aromatic medicinal plants, Agastache mexicana (Lamiaceae) and A. m. subsp. xolocotziana, widely used in Mexican traditional medicine for the treatment of gastrointestinal ailments and for their sedative effect. Different populations of A. mexicana along a gradient of domestication are found in the foothills of the Popocatepetl volcano of central Mexico, while in this same area the subsp. xolocotziana grows only in the cultivation, possibly a product of hybridization between A. mexicana and Agastache palmeri. This study links ethnobotanical, morpho-physiological, and phytochemical evidence to document the domestication of both taxa as well as elucidates the possible hybrid origin of the subsp. xolocotziana. Method We analyze three groups of data derived from (1) 80 semi-structured interviews aimed at documenting the selection criteria related to the use and management of A. mexicana; (2) a cultivation experiment under homogeneous conditions, evaluating 21 floral, vegetative, and seed characters (that were important according to ethnobotanical information) in 97 plants corresponding to 13 populations of the taxa under study; and (3) the chemical profiles of the essential oils of these plants by means of a thin-layer chromatography. Results By linking the three types of evidence, two evolutionary processes are distinguished: (1) A. mexicana occurs in the encouraged-cultivated phases of the domestication gradient and (2) A. m. subsp. xolocotziana may have originated through inbreeding depression or hybridization. These two cultivated plants show a domestication syndrome based upon organoleptic differentiation due to their dissimilar phytochemical composition and gigantism in flowers, seeds, and rhizomes (the last enhancing their asexual reproductive capacity). In addition to this, A. mexicana exhibits more intense floral pigmentation and foliar gigantism while subsp. xolocotziana presents floral albinism and partial seed sterility. Conclusion Two divergent evolutionary processes are reported for the domestication of A. mexicana as a result of the intensification of its use and management. The selection processes of these plants have resulted in alternation of the organoleptic properties based upon the divergence of the phytochemical composition. Also, gigantism has been selected in culturally preferred plant parts and in correlated structures. The preceding characteristics reinforce the joint use of these plants in infusion in Mexican traditionalmedicine for the treatment of gastrointestinal diseases and for their sedative effects.

We compiled an updated database of all Agave species found in Mexico and analyzed it with specific criteria according to their biological parameters to evaluate the conservation and knowledge status of each species. Analyzing the present status of all Agave species not only provides crucial information for each species, but also helps determine which ones require special protection, especially those which are heavily used or cultivated for the production of distilled beverages. We conducted an extensive literature review search and compiled the conservation status of each species using mainstream criteria by IUCN. The information gaps in the database indicate a lack of knowledge and research regarding specific Agave species and it validates the need to conduct more studies on this genus. In total, 168 Agave species were included in our study, from which 89 are in the subgenus Agave and 79 in the subgenus Littaea. Agave lurida and A. nizandensis, in the subgenus Agave and Littaea, respectively, are severely endangered, due to their endemism, lack of knowledge about pollinators and floral visitors, and their endangered status according to the IUCN Red List. Some species are at risk due to the loss of genetic diversity resulting from production practices (i.e., Agave tequilana), and others because of excessive and unchecked overharvesting of wild plants, such as A. guadalajarana, A. victoriae-reginae, A. kristenii, and others. Given the huge economic and ecological importance of plants in the genus Agave, our review will be a milestone to ensure their future and continued provision of ecosystem services for humans, as well as encouraging further research in Agave species in an effort to enhance awareness of their conservation needs and sustainable use, and the implementation of eco-friendly practices in the species management.

Leptonycteris yerbabuenae, the lesser long-nosed bat is an abundant migratory nectar-feeding bat found in most of Mexico, and in some areas of northern Central America and small sections of southwestern USA. We analyzed the distribution of the maternal and paternal lineages of this species with phylogeographic methods based on two mitochondrial markers, Cyt-b and D-loop, and a marker located in the Y chromosome, DBY. We obtained tissue samples from 220 individuals from 23 localities. Levels of genetic diversity (haplotype diversity, Hd) were high (Cyt-b = 0.757; D-loop = 0.8082; DBY = 0.9137). No clear patterns of population genetic structure were found for mitochondrial markers, while male genetic differentiation suggested the presence of two lineages: one from Mexican Pacific coast states and another from central-southern Mexico; in accordance to strong male philopatry and higher female migration. We used genealogical reconstructions based on Bayesian tools to calculate divergence times, and to test coalescent models to explain changes in L. yerbabuenae historical demography. Our results show that recent demographic changes were consistent with global climatic changes (∼130,000 kyr ago for Cyt-b and ∼160,000 kyr for D-loop) and divergence times dated from molecular genealogies exhibited older divergence times, Cyt-b (4.03 mya), D-loop (10.26 mya) and DBY (12.23 mya). Accordingly, the female lineage underwent demographic expansion associated to Pleistocene climate change, whereas the male lineage remained constant.

The behavior of bees is modulated by the presence of other bees and potentially by the visual information transmitted by the different body positions of bees while visiting flowers. We tested whether bee body position promoted the attraction and/or antagonistic behavior of con- and hetero-specific bees that interacted on prickly pear flowers of Opuntia huajuapensis. To test this, we placed dummy model bees of Apis mellifera and the native Lithurgus littoralis in flowers in three common body positions: alert, feeding, and horizontal. The results showed that dummy model bees in feeding and horizontal body positions attracted A. mellifera bees, while the alert position attracted native male L. littoralis. Male L. littoralis bees spent more time attacking model bees in horizontal and alert positions. The position of dummy bees also influenced response times. Bees of A. mellifera responded fastest to L. littoralis in the alert and horizontal position, male L. littoralis responded fastest to con-specific bees in the alert and feeding position, and female L. littoralis responded fastest to A. mellifera bees in the feeding position. A. mellifera reacted fastest to their con-specific bees in the alert and horizontal body positions. Our results demonstrate, for the first time in bees, that the position of individuals on a floral resource provides important visual information that modulates bee behavior, and illuminates aspects that likely have implications for bees in access to floral resources.

Studies of domestication genetics enrich our understanding of how domestication shapes genetic and morphological diversity. We characterized patterns of genetic variation in two independently domesticated pumpkins and their wild progenitors to assess and compare genetic consequences of domestication. To compare genetic diversity pre- and post-domestication and to identify genes targeted by selection during domestication, we analyzed ∼15,000 SNPs of 48 unrelated accessions, including wild, landrace, and improved lines for each of two pumpkin species, Cucurbita argyrosperma and Cucurbita maxima. Genetic diversity relative to its wild progenitor was reduced in only one domesticated subspecies, C. argyrosperma ssp. argyrosperma. The two species have different patterns of genetic structure across domestication status. Only 1.5% of the domestication features identified for both species were shared between species. These findings suggest that ancestral genetic diversity, wild-crop gene flow, and domestication practices shaped the genetic diversity of two similar Cucurbita crops in different ways, adding to our understanding of how genetic diversity changes during the processes of domestication and how trait improvement impacts the breeding potential of modern crops.

La domesticación de plantas y animales permite estudiar diferentes procesos evolutivos, como la selección, adaptación y especiación. En este artículo se describen avances recientes en el estudio de las calabazas, las cuales constituyen el género Cucurbita (Cucurbitaceae) siendo un grupo de plantas herbáceas americanas que incluyen entre 12 y 15 especies. Cucurbita ha tenido seis eventos de domesticación, de los cuales cuatro sucedieron en México. Este es un género relativamente reciente, que surgió en Norte América hace 16 millones de años y sus especies cultivadas mantienen una alta variación genética; Cucurbita pepo es la especie que presenta mayor variación genética,variación asociada a dos domesticaciones independientes, una en el norte de México, y otra en el Sureste de los Estados Unidos. En otra especie, Cucurbita argyrosperma, sus poblaciones de la Península de Yucatán, representan una poza genética diferenciada del resto de la especie. El estudio del genoma de C. argyrosperma y taxa cercanos ha revelado las regiones de su genoma asociadas a la domesticación. Las poblaciones de las especies de este género representan una fuente de importantes recursos genéticos frente al cambio climático y constituyen un buen sistema para el estudio de la domesticación y de diferentes procesos evolutivos.

Gene flow among crops and their wild relatives is an active study area in evolutionary biology and horticulture, because genetic exchange between them may impact their evolutionary trajectories and increase the genetic variation of the cultivated lineages. Mexico is a center of diversity for the genus Cucurbita that includes pumpkins, squash and gourds. Gene flow between domesticated and wild species has been reported as common in Cucurbita; but gene flow among populations of C. pepo ssp. pepo from Mexico and its wild relative has not been studied. We used 2,061 SNPs, derived from tunable genotyping by sequencing (tGBS) to estimate gene flow among 14 Mexican traditional landraces of C. pepo ssp. pepo, also including individuals from five improved cultivars of C. pepo ssp. pepo and C. pepo ssp. ovifera var. ovifera, and individuals of their wild relative C. pepo ssp. fraterna. We found moderate to high levels of genetic diversity, and low to moderate genetic differentiation. In the test of introgression between lineages, we found that all possible arrangements for ancestral and derived sites between the lineages showed similar frequencies; thus, incomplete lineage sorting, but also gene flow, might be taking place in C. pepo. Overall, our results suggest that gene flow between these subspecies and cultigens, incomplete lineage sorting and the retention of ancestral characters shaped the evolutionary trajectory of C. pepo in its area of origin and diversification. In addition, we found evidence of the use of Mexican landraces as genetic material for the improvement of commercial cultivars. The landraces of Mexico are an important source of genetic diversity for C. pepo, which has been preserved both by management practices of small farmers and by the natural gene flow that exists between the different crop fields of the region.

Anthropogenic perturbations introduce novel selective pressures to natural environments, impacting the genomic variability of organisms and thus altering the evolutionary trajectory of populations. Water overexploitation for agricultural purposes and defective policies in Cuatro Cienegas, Coahuila, Mexico, have strongly impacted its water reservoir, pushing entire hydrological systems to the brink of extinction along with their native populations. Here, we studied the effects of continuous water overexploitation on an environmental aquatic lineage of Pseudomonas otitidis over a 13-year period which encompasses three desiccation events. By comparing the genomes of a population sample from 2003 (original state) and 2015 (perturbed state), we analyzed the demographic history and evolutionary response to perturbation of this lineage. Through coalescent simulations, we obtained a demographic model of contraction-expansion-contraction which points to the occurrence of an evolutionary rescue event. Loss of genomic and nucleotide variation alongside an increment in mean and variance of Tajima’s D, characteristic of sudden population expansions, support this observation. In addition, a significant increase in recombination rate (R/θ) was observed, pointing to horizontal gene transfer playing a role in population recovery. Furthermore, the gain of phosphorylation, DNA recombination, small-molecule metabolism and transport and loss of biosynthetic and regulatory genes suggest a functional shift in response to the environmental perturbation. Despite subsequent sampling events in the studied site, no pseudomonad was found until the lagoon completely dried in 2017. We speculate about the causes of P. otitidis final decline or possible extinction. Overall our results are evidence of adaptive responses at the genomic level of bacterial populations in a heavily exploited aquifer.

Due to the recent increase in demand for agave-based beverages, many wild agave populations have experienced rapid decline and fragmentation, whereas cultivated plants are now managed at monocultural plantations, in some cases involving clonal propagation. We examined the relative effect of migration, genetic drift, natural selection and human activities on the genetic repertoire of Agave angustifolia var. pacifica, an agave used for bacanora (an alcoholic spirit similar to tequila) production in northwestern Mexico. We sampled 34 wild and cultivated sites and used over eleven thousand genome-wide SNPs. We found shallow genetic structure among wild samples, although we detected differentiation between coastal and inland sites. Surprisingly, no differentiation was found between cultivated and wild populations. Moreover, we detected moderate inbreeding (FIS ~ 0.13) and similar levels of genomic diversity in wild and cultivated agaves. Nevertheless, the cultivated plants had almost no private alleles and presented evidence of clonality. The overall low genetic structure in A. angustifolia var. pacifica is apparently the result of high dispersibility promoted by pollinators and the possibility of clonal reproduction. Incipient cultivation history and reliance on wild seeds and plants are probably responsible for the observed patterns of high genetic connectivity and considerable diversity in cultivated samples.

Agave sensu lato is one of the most diverse and complex genera of Asparagaceae, with more than 250 species. The morphological, ecological, and evolutionary diversity of the group has complicated its taxonomical study. We conducted phylogenetic analyses of DNA sequence data to reconstruct the phylogenetic relationships of the Agave genus. We included 107 species of the Asparagaceae family from which 83 correspond to the Agave sensu lato clade (Agave sensu stricto + Polianthes + Manfreda and Prochnyanthes, which together represent 30% of the genus) and as outgroups the genera Dasylirion, Hesperoyucca, Chlorogalum, Camassia, Hesperaloe, Yucca, Beschorneria, and Furcraea, in order to estimate the age and propose the history of their diversification. Previous studies postulated the relevance of the Miocene in the speciation rates of the agaves, as well as the relevance of the type of inflorescence in its diversification. However, these assertions have not been well supported. The analysis of chloroplast regions resulted in low resolution, which could be the consequence of the few variable sites. On the other hand, the internal transcribed spacer (ITS) implemented in our analysis ensued in higher resolution and better support values. Our phylogenetic analyses recovered five groups; one is the Striatae group, which is the sister group to Agave sensu stricto clade. Within this clade, we found three main groups with high support; these groups are not related with previous morphological proposals. We also analyzed the dates of origin and diversification rates. A Bayesian analysis of macroevolutionary mixtures indicated two significant shifts; the first was identified at 6.18 Ma, where the speciation rate increased to 4.10 species/Mya, this shift occurred during the late Miocene period, characterized by the emergence of arid biomes in North America. The second was identified at a stem age of 2.68 Ma where the speciation rate increased to 6.04 species/Mya. Concerning the ancestral reconstruction state of the inflorescence type in the Agave sensu stricto clade, the spike inflorescence character was predominant in the early-diverging groups, whereas the late-diverging groups present panicle inflorescences as the predominant character and higher speciation rates.

Dimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton and bacteria, is primarily degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: (1) a recent common ancestor of DmdA and GcvT, (2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and (3) an enzymatic adaptation for utilizing DMSP in marine bacteria prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur-rich atmosphere and anoxic ocean, compared to recent Roseobacter eco-orthologs (orthologs performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.

Massive parallel sequencing (MPS) is revolutionizing the field of molecular ecology by allowing us to understand better the evolutionary history of populations and species, and to detect genomic regions that could be under selection. However, the economic and computational resources needed generate a tradeoff between the amount of loci that can be obtained and the number of populations or individuals that can be sequenced. In this work, we analyzed and compared two simulated genomic datasets fitting a hierarchical structure, two extensive empirical genomic datasets, and a dataset comprising microsatellite information. For all datasets, we generated different subsampling designs by changing the number of loci, individuals, populations, and individuals per population to test for deviations in classic population genetics parameters (HS, FIS, FST). For the empirical datasets we also analyzed the effect of sampling design on landscape genetic tests (isolation by distance and environment, central abundance hypothesis). We also tested the effect of sampling a different number of populations in the detection of outlier SNPs. We found that the microsatellite dataset is very sensitive to the number of individuals sampled when obtaining summary statistics. FIS was particularly sensitive to a low sampling of individuals in the simulated, genomic, and microsatellite datasets. For the empirical and simulated genomic datasets, we found that as long as many populations are sampled, few individuals and loci are needed. For the empirical datasets, we found that increasing the number of populations sampled was important in obtaining precise landscape genetic estimates. Finally, we corroborated that outlier tests are sensitive to the number of populations sampled. We conclude by proposing different sampling designs depending on the objectives.

In the last decade, genomics and the related fields of transcriptomics and epigenomics have revolutionized the study of the domestication process in plants and animals, leading to new discoveries and new unresolved questions. Given that some domesticated taxa have been more studied than others, the extent of genomic data can range from vast to nonexistent, depending on the domesticated taxon of interest. This review is meant as a rough guide for students and academics that want to start a domestication research project using modern genomic tools, as well as for researchers already conducting domestication studies that are interested in following a genomic approach and looking for alternate strategies (cheaper or more efficient) and future directions. We summarize the theoretical and technical background needed to carry out domestication genomics, starting from the acquisition of a reference genome and genome assembly, to the sampling design for population genomics, paleogenomics, transcriptomics, epigenomics and experimental validation of domestication-related genes. We also describe some examples of the aforementioned approaches and the relevant discoveries they made to understand the domestication of the studied taxa.

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 (FST = 0.928, GST = 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.

The widespread use of genomic tools has allowed for a deeper understanding of the genetics and the evolutionary dynamics of domestication. Recent studies have suggested that multiple domestications and introgression are more common than previously thought. However, the ability to correctly infer the many aspects of domestication process depends on having an adequate representation of wild relatives. Cultivated maize (Zea mays ssp. mays) is one of the most important crops in the world, with a long and a relatively well-documented history of domestication. The current consensus points towards a single domestication event from teosinte Zea mays ssp. parviglumis from the Balsas Basin in Southwestern Mexico. However, the underlying diversity of teosintes from Z. mays ssp. parviglumis and Zea mays ssp. mexicana was not taken into account in early studies. We used 32 739 single nucleotide polymorphisms (SNPs) obtained from 29 teosinte populations and 43 maize landraces to explore the relationship between wild and cultivated members of Zea. We then inferred the levels of gene flow among teosinte populations and maize, the degree of population structure of Zea mays subspecies, and the potential domestication location of maize. We confirmed a strong geographic structure within Z. mays ssp. parviglumis and documented multiple gene flow events with other members of the genus, including an event between Z. mays ssp. mexicana and maize. Our results suggest that the likely ancestor of maize may have been domesticated in Jalisco or in the southern Pacific Coast and not in the Balsas Basin as previously thought. In this context, different populations of both teosinte subspecies have contributed to modern maize's gene pool. Our results point towards a long period of domestication marked by gene flow with wild relatives, confirming domestication as long and ongoing process.

The present dataset comprises 36,931 SNPs genotyped in 46 maize landraces native to Mexico as well as the teosinte subspecies Zea maiz ssp. parviglumis and ssp. mexicana. These landraces were collected directly from farmers mostly between 2006 and 2010. We accompany these data with a short description of the variation within each landrace, as well as maps, principal component analyses and neighbor joining trees showing the distribution of the genetic diversity relative to landrace, geographical features and maize biogeography. High levels of genetic variation were detected for the maize landraces (HE = 0.234 to 0.318 (mean 0.311), while slightly lower levels were detected in Zea m. mexicana and Zea m. parviglumis (HE = 0.262 and 0.234, respectively). The distribution of genetic variation was better explained by environmental variables given by the interaction of altitude and latitude than by landrace identity. This dataset is a follow up product of the Global Native Maize Project, an initiative to update the data on Mexican maize landraces and their wild relatives, and to generate information that is necessary for implementing the Mexican Biosafety Law. Keywords: Maize, Teosinte, Maize SNP50K BeadChip, Mexican landraces, Proyecto Global de Maíces Nativos

To date, it remains unclear how anthropogenic perturbations influence the dynamics of microbial communities, what general patterns arise in response to disturbance, and whether it is possible to predict them. Here, we suggest the use of microbial mats as a model of study to reveal patterns that can illuminate the ecological processes underlying microbial dynamics in response to stress. We traced the responses to anthropogenic perturbation caused by water depletion in microbial mats from Cuatro Cienegas Basin (CCB), Mexico, by using a time-series spatially resolved analysis in a novel combination of three computational approaches. First, we implemented MEBS (Multi-genomic Entropy-Based Score) to evaluate the dynamics of major biogeochemical cycles across spatio-temporal scales with a single informative value. Second, we used robust Time Series-Ecological Networks (TS-ENs) to evaluate the total percentage of interactions at different taxonomic levels. Lastly, we utilized network motifs to characterize specific interaction patterns. Our results indicate that microbial mats from CCB contain an enormous taxonomic diversity with at least 100 phyla, mainly represented by members of the rare biosphere (RB). Statistical ecological analyses point out a clear involvement of anaerobic guilds related to sulfur and methane cycles during wet versus dry conditions, where we find an increase in fungi, photosynthetic, and halotolerant taxa. TS-ENs indicate that in wet conditions, there was an equilibrium between cooperation and competition (positive and negative relationships, respectively), while under dry conditions there is an over-representation of negative relationships. Furthermore, most of the keystone taxa of the TS-ENs at family level are members of the RB and the microbial mat core highlighting their crucial role within the community. Our results indicate that microbial mats are more robust to perturbation due to redundant functions that are likely shared among community members in the highly connected TS-ENs with density values close to one (≈0.9). Finally, we provide evidence that suggests that a large taxonomic diversity where all community members interact with each other (low modularity), the presence of permanent of low-abundant taxa, and an increase in competition can be potential buffers against environmental disturbance in microbial mats.

Microbial interactions play a key role in ecosystem functioning, with nutrient availability as an important determinant. Although phylogenetically distant bacteria and fungi commonly co-occur in nature, information on their cross-kingdom interactions under unstable, extreme environments remains poor. Hence, the aims of this work were to evaluate potential in vitro interactions among fungi and bacteria isolated from a phosphorous oligotrophic aquatic system in the Cuatro Ciénegas Basin, Mexico, and to test the nutrients-based shifts. We assessed growth changes in bacteria (Aeromonas and Vibrio) and fungi (Coprinellus micaceus, Cladosporium sp., and Aspergillus niger) on co-cultures in relation to monocultures under diverse nutrient scenarios on Petri dishes. Interactions were explored using a network analysis, and a metabolome profiling for specific taxa. We identified nutrient-dependent patterns, as beneficial interactions dominated in low-nutrients media and antagonistic interactions dominated in rich media. This suggests that cross-kingdom synergistic interactions might favor microbial colonization and growth under low nutrient conditions, representing an adaptive trait to oligotrophic environments. Moreover, our findings agree with the stress-gradient hypothesis, since microbial interactions shifted from competition to cooperation as environmental stress (expressed as low nutrients) increased. At a functional level consistent differences were detected in the production of secondary metabolites, agreeing with plate bioassays. Our results based on culture experiments, provides evidence to understand the complexity of microbial dynamics and survival in phosphorous-depleted environments.

Mite-fungal interactions play a key role in structuring core ecosystem processes such as nutrient dynamics. Despite their ecological relevance, these cross-kingdom interactions remain poorly understood particularly in extreme environments. Herein, we investigated feeding preferences of a novel genetic lineage of aquatic oribatids obtained from an oligotrophic freshwater system in the Cuatro Ciénegas Basin (CCB) within the Chihuahuan Desert, Mexico. During in vitro diet preference bioassays, transient aquatic microfungi (Aspergillus niger, Talaromyces sp., and Pleosporales sp.) recovered from the same mesocosm samples were offered individually and simultaneously to mites. Gut content was analyzed using classic plating and culture-independent direct PCR (focusing on the fungal barcoding region) methods. Our results indicated that oribatids fed on all tested fungal isolates, yet the profusely developing A. niger was preferentially consumed with all fungal components being digested. This feeding habit is particularly interesting since A. niger has been reported as an unsuitable dietary element for population growth, being consistently avoided by mites in previous laboratory experiments. It is possible that our mites from the CCB have adapted to exploit available resources within this oligotrophic site. This work confirms the trophic relationship between microfungi and mites, two rarely investigated major components of the microbial community, shedding light on the niche dynamics under low-nutrient conditions.

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.

Analyses of genetic variation allow understanding the origin, diversification and genetic resources of cultivated plants. Domesticated taxa and their wild relatives are ideal systems for studying genetic processes of plant domestication and their joint is important to evaluate the distribution of their genetic resources. Such is the case of the domesticated subspecies C. argyrosperma ssp. argyrosperma, known in Mexico as calabaza pipiana, and its wild relative C. argyrosperma ssp. sororia. The main aim of this study was to use molecular data (microsatellites) to assess the levels of genetic variation and genetic differentiation within and among populations of domesticated argyrosperma across its distribution in Mexico in comparison to its wild relative, sororia, and to identify environmental suitability in previously proposed centers of domestication. We analyzed nine unlinked nuclear microsatellite loci to assess levels of diversity and distribution of genetic variation within and among populations in 440 individuals from 19 populations of cultivated landraces of argyrosperma and from six wild populations of sororia, in order to conduct a first systematic analysis of their genetic resources. We also used species distribution models (SDMs) for sororia to identify changes in this wild subspecies’ distribution from the Holocene (∼6,000 years ago) to the present, and to assess the presence of suitable environmental conditions in previously proposed domestication sites. Genetic variation was similar among subspecies (HE = 0.428 in sororia, and HE = 0.410 in argyrosperma). Nine argyrosperma populations showed significant levels of inbreeding. Both subspecies are well differentiated, and genetic differentiation (FST) among populations within each subspecies ranged from 0.152 to 0.652. Within argyrosperma we found three genetic groups (Northern Mexico, Yucatan Peninsula, including Michoacan and Veracruz, and Pacific coast plus Durango). We detected low levels of gene flow among populations at a regional scale (

Nutrient availability and ratios can play an important role in shaping microbial communities of freshwater ecosystems. The Cuatro Ciénegas Basin (CCB) in Mexico is a desert oasis where, perhaps paradoxically, high microbial diversity coincides with extreme oligotrophy. To better understand the effects of nutrients on microbial communities in CCB, a mesocosm experiment was implemented in a stoichiometrically imbalanced pond, Lagunita, which has an average TN:TP ratio of 122 (atomic). The experiment had four treatments, each with five spatial replicates – unamended controls and three fertilization treatments with different nitrogen:phosphorus (N:P) regimes (P only, N:P = 16 and N:P = 75 by atoms). In the water column, quantitative PCR of the 16S rRNA gene indicated that P enrichment alone favored proliferation of bacterial taxa with high rRNA gene copy number, consistent with a previously hypothesized but untested connection between rRNA gene copy number and P requirement. Bacterial and microbial eukaryotic community structure was investigated by pyrosequencing of 16S and 18S rRNA genes from the planktonic and surficial sediment samples. Nutrient enrichment shifted the composition of the planktonic community in a treatment-specific manner and promoted the growth of previously rare bacterial taxa at the expense of the more abundant, potentially endemic, taxa. The eukaryotic community was highly enriched with phototrophic populations in the fertilized treatment. The sediment microbial community exhibited high beta diversity among replicates within treatments, which obscured any changes due to fertilization. Overall, these results showed that nutrient stoichiometry can be an important factor in shaping microbial community structure.

The phylum Actinobacteria constitutes one of the largest and anciently divergent phyla within the Bacteria domain. Actinobacterial diversity has been thoroughly researched in various environments due to its unique biotechnological potential. Such studies have focused mostly on soil communities, but more recently marine and extreme environments have also been explored, finding rare taxa and demonstrating dispersal limitation and biogeographic patterns for Streptomyces. To test the distribution of Actinobacteria populations on a small scale, we chose the extremely oligotrophic and biodiverse Cuatro Cienegas Basin (CCB), an endangered oasis in the Chihuahuan desert to assess the diversity and uniqueness of Actinobacteria in the Churince System with a culture-dependent approach over a period of three years, using nine selective media. The 16S rDNA of putative Actinobacteria were sequenced using both bacteria universal and phylum-specific primer pairs. Phylogenetic reconstructions were performed to analyze OTUs clustering and taxonomic identification of the isolates in an evolutionary context, using validated type species of Streptomyces from previously phylogenies as a reference. Rarefaction analysis for total Actinobacteria and for Streptomyces isolates were performed to estimate species’ richness in the intermediate lagoon (IL) in the oligotrophic Churince system. A total of 350 morphologically and nutritionally diverse isolates were successfully cultured and characterized as members of the Phylum Actinobacteria. A total of 105 from the total isolates were successfully subcultured, processed for DNA extraction and 16S-rDNA sequenced. All strains belong to the order Actinomycetales, encompassing 11 genera of Actinobacteria; the genus Streptomyces was found to be the most abundant taxa in all the media tested throughout the 3-year sampling period. Phylogenetic analysis of our isolates and another 667 reference strains of the family Streptomycetaceae shows that our isolation effort produced 38 unique OTUs in six new monophyletic clades. This high biodiversity and uniqueness of Actinobacteria in an extreme oligotrophic environment, which has previously been reported for its diversity and endemicity, is a suggestive sign of microbial biogeography of Actinobacteria and it also represents an invaluable source of biological material for future ecological and bioprospecting studies.

Abstract The increasing aridity during the Last Glacial Maximum (LGM) has been proposed as a major factor affecting Neotropical species. The character and intensity of this change, however, remains the subject of ongoing debate. This review proposes an approach to test contrasting paleoecological hypotheses by way of their expected demographic and genetic effects on Neotropical cloud forest species. We reviewed 48 paleoecological records encompassing the LGM in the Neotropics. The records show contrasting evidence regarding the changes in precipitation during this period. Some regions remained fairly moist and others had a significantly reduced precipitation. Many paleoecological records within the same region show apparently conflicting evidence on precipitation and forest stability. From these data, we propose and outline two demographic/genetic scenarios for cloud forests species based on opposite precipitation regimes: the dry refugia and the moist forests hypotheses. We searched for studies dealing with the population genetic structure of cloud forest and other montane taxa and compared their results with the proposed models. To date, the few available molecular studies show insufficient genetic evidence on the predominance of glacial aridity in the Neotropics. In order to disentangle the climatic history of the Neotropics, the present study calls for a general multi‐disciplinary approach to conduct future phylogeographic studies. Given the contradictory paleoecological information, population genetic data on Neotropical cloud forest species should be used to explicitly test the genetic consequences of competing paleoecological models.

La teoría de la genética de poblaciones surgió hace más de 80 años y nos permite explicar los patrones de variación genética dentro y entre las poblaciones que forman a las especies en términos de las fuerzas evolutivas. Este programa de investigación generó las preguntas que se han abordado empíricamente mediante marcadores moleculares desde hace medio siglo. Una pregunta fundamental ha sido hasta dónde un conjunto reducido de loci es o no representativo del efecto de las fuerzas evolutivas, sobre todo el genoma de una especie. Esto ha llevado al desarrollo creciente de aproximaciones que permitan conocer de manera representativa los niveles de variación genética en las poblaciones naturales, dando origen a la genómica de poblaciones. En años recientes, las técnicas de secuenciación masiva, llamadas Next generation sequencing, o next-gen, han permitido obtener datos de grandes secciones del genoma de diferentes especies, sin que sea un requisito conocer marcadores previos. Así, al comparar los genomas de muchos individuos de diferentes poblaciones, tenemos acceso al archivo de su historia evolutiva, que nos habla del complejo y dinámico balance en el tiempo entre la selección natural y las otras fuerzas evolutivas de carácter neutral, como la deriva y el flujo génico. La existencia de enormes cantidades de información ha requerido el desarrollo de nuevas herramientas estadísticas y bioinformáticas para su análisis. Diversas disciplinas se han visto beneficiadas de estos desarrollos. Para la biología evolutiva se abre la posibilidad de estudiar de manera más precisa y clara los patrones adaptativos de la variación. Tener genomas anotados y loci bien mapeados es relevante y arduo, pero el desarrollo técnico hace que lo anterior sea cada vez más plausible, y el reto será ser capaces de plantear preguntas adecuadas para hacer inferencias del mar de información disponible. El uso de una perspectiva evolutiva y de genética de poblaciones, enriquecerá a la genómica, de la misma manera que los datos genómicos nos ayudarán a avanzar en el desarrollo del programa iniciado por Theodosius Dobzhansky a mediados del siglo pasado.

We analyzed the changes in composition, diversity and structure of trees and shrubs along a successional gradient in southwest Mexico. Early stages were dominated by typical pioneer species but species of mature forests were present throughout the chronosequence, and therefore the species plant distribution between stages may be explained by the initial floristic composition model. Because sites from all stages had similar number of species, our study does not support the intermediate levels of disturbance hypothesis. Contrary to the patterns observed in other dry forests, the mature stages presented a relatively simple structure complexity compared to that of intermediate forests. This resulted from a few dominant species which are usually present in mature forests with some degree of perturbation. According to the polyclimax hypothesis, diversity of the mature forests appears to be influenced by local soil conditions, microclimates and biotic factors. Our study supports this idea because local conditions vary between sites and the dominant species of the late stages were different between stands. The conservation and management plans should be directed to different successional stages and not only to single patches in order to ensure the conservation of regional biodiversity.Se analizó la composición, diversidad y estructura de los árboles y arbustos en un un gradiente sucesional en el suroeste de México. Las etapas tempranas presentaron mayor dominancia de especies típicas pioneras, pero especies de bosques maduros se encontraron en todos los sitios, tal como predice el modelo de la composición florística inicial. Debido a que todos los sitios tuvieron una riqueza similar, nuestro estudio no apoya la hipótesis de la perturbación intermedia. Contrario a los patrones observados en otros bosques secos, la estructura de la vegetación resultó menos compleja en las etapas maduras en comparación con las intermedias. Esto es resultado de especies dominantes que se encuentran en bosques maduros con algún grado de perturbación. De acuerdo con la teoría del policlímax, la diversidad en bosques maduros es resultado del microclima, condiciones edáficas y factores bióticos. Nuestros resultados apoyan esta idea ya que las condiciones locales varían entre sitios y las especies dominantes de las etapas tardías fueron diferentes entre los sitios. Los esfuerzos para la conservación de áreas, así como los planes de manejo deben contemplar diferentes etapas sucesionales y no sólo parches aislados, con el fin de asegurar la conservación de la biodiversidad regional.

Background Relationships between floral biology and pollinator behavior are important to understanding species diversity of hemiparasitic Psittacanthus mistletoes (c. 120 species). We aimed to investigate trait divergence linked to pollinator attraction and reproductive isolation (RI) in two hummingbird-pollinated and bird-dispersed Psittacanthus species with range overlap. Methods We investigated the phylogenetic relationships, floral biology, pollinator assemblages, seed dispersers and host usage, and the breeding system and female reproductive success of two sympatric populations of P. calyculatus and P. auriculatus, and one allopatric population of P. calyculatus. Flowers in sympatry were also reciprocally pollinated to assess a post-mating component of RI. Results Hummingbird assemblages differed between calyculatus populations, while allopatric plants of calyculatus opened more but smaller flowers with longer lifespans and produced less nectar than those in sympatry. Bayesian-based phylogenetic analysis indicated monophyly for calyculatus populations (i.e. both populations belong to the same species). In sympatry, calyculatus plants opened more and larger flowers with longer lifespans and produced same nectar volume than those of auriculatus; populations shared pollinators but seed dispersers and host usage differed between species. Nectar standing crops differed between sympatric populations, with lower visitation in calyculatus. Hand pollination experiments indicated a predominant outcrossing breeding system, with fruit set after interspecific pollination two times higher from calyculatus to auriculatus than in the opposite direction. Conclusions Given the low genetic differentiation between calyculatus populations, observed trait divergence could have resulted from changes regarding the local communities of pollinators and, therefore, expected divergence for peripheral, allopatric populations. Using RI estimates, there were fewer heterospecific matings than expected by chance in P. calyculatus (RI4A = 0.629) as compared to P. auriculatus (RI4A = 0.20). When considering other factors of ecological isolation that affect co-occurrence, the RI4C values indicate that isolation by hummingbird pollinators was less effective (0.20) than isolation by host tree species and seed dispersers (0.80 and 0.60, respectively), suggesting that host usage is the most important ecological isolation factor between the two species. Accordingly, the absolute and relative cumulative strength values indicated that the host tree species’ barrier is currently contributing the most to maintaining these species in sympatry.

The Cuatro Ciénegas Basin (CCB) comprises several oligotrophic aquatic ecosystems limited by phosphorus. These aquatic systems are dominated by a high prokaryotic diversity, shaped by the stress of low nutrient supplies and interspecific competition. Although fungi constitute a diverse and important component of microbial diversity, the microfungal diversity in the CCB remains to be unveiled. With the aim to explore microfungal diversity and ecological patterns in this area, we present the first investigation analyzing cultivable taxa from sediment and water, as well as lignocellulolytic taxa obtained from incubated submerged plant debris, and wood panels in three contrasting freshwater systems in the CCB: Churince, Becerra and Pozas Rojas. We chose a culture-based approach to analyze sediment and water samples in order to obtain fungal cultures, providing opportunities for a posteriori studies, and the possibility of ex situ preservation of the diversity. We evaluated sequence data from the nuclear ribosomal internal transcribed spacer including the 5.8 rDNA region for 126 isolates, revealing 37 OTUs. These OTUs were phylogenetically affiliated to several genera in the fungal phyla: Zygomycota, Basidiomycota, and Ascomycota. We recorded two OTUs with saline affinity, agreeing with previous findings on the prokaryotic communities with ancestral marine resemblances. All the studied systems showed moderate diversity levels, however discrepancies among the diversity indexes were observed, due to the occurrence of abundant taxa in the samples. Our results indicated that lignocellulolytic microfungal communities are dominated by transient fungal taxa, as resident species were not recorded perhaps as a result of the long-term strong competition with the highly adapted prokaryotic community. Moreover, the obtained microfungal taxa occurred mostly on the resident plant debris, rather than submerged wood panels, perhaps as a result of the high adaptation to specific environmental conditions. In conclusion, the CCB possess a moderate taxonomical diversity compared to other arid environments, probably as a result of high selective pressures. Nonetheless, due to high spatial and temporal heterogeneity, the functional fungal diversity was considerable as predicted by the intermediate disturbance hypothesis. Decisively, the assessment of microfungal diversity freshwater systems is relevant, since this ecological group of microorganisms represents an important indicator of trophic complexity and biotic interactions among microbial communities, having important implications for understanding eukaryotic survival at the oligotrophic limit for life.