Phylogenetic discordance and integrative species delimitation in the Mammillaria haageana species complex (Cactaceae).

Species complexes consist of very close phylogenetic relatives, where morphological similarities make it difficult to distinguish between them using traditional taxonomic methods. Here, we focused on the long-standing challenge of species delimitation in the Mammillaria haageana complex, a group that presents great morphological diversity that makes its taxonomy a puzzle. Our work integrates genomic, morphological, and ecological data to establish the taxonomic limits in the M. haageana complex, and we also studied the evolutionary relationships with the remainder of the M. ser. Supertextae species. Our genetic analyses, as well as morphological and ecological evidence, led us to propose that the M. haageana complex is made up of six distinct entities (M. acultzingensis, M. conspicua, M. haageana, M. lanigera, M. meissneri, and M. san-angelensis), mainly as a result of ecological speciation. A recent taxonomic proposal considered these taxa as a single species; therefore, we propose their recognition at the species level. Our results also show a high level of incomplete lineage sorting rather than reticulation, which is especially likely in recently diverged species such as those comprising M. ser. Supertextae. The species hypotheses proposed here may be useful in future extinction risk assessments and conservation strategies.

Contribution of Morphoanatomic Characters to the Taxonomy of the Genus LAELIA (Orchidaceae) in Mexico and Their Implication in Environmental Adaptation.

The Laeliinae Subtribe (Epidendroideae-Orchidaceae) is exclusively Neotropical, composed of 43 genera and 1466 species, presenting great floral and vegetative diversity. The genus Laelia has restricted geographic distribution, with species in Brazil and Mexico. However, in molecular studies, the Brazilian species have not been included despite remarkably similar floral structures in both Mexican and Brazilian groups of species. The main objective of the present study is to analyze vegetative structural characters of 12 species of Laelia in Mexico to find similarities to recognize them as a taxonomic group and their relationship with possible ecological adaptations. This work supports the proposal to recognize 12 species of Laelias from Mexico as a taxonomic group (except for the new species recognized as Laelia dawsonii J. Anderson), since a strong similarity was found, translated by 90% of structural characters shared by the Mexican Laelias, given the relationship between the structural characters and the altitudinal distribution in which the groups of Mexican Laelias species are found. We propose that Laelias of Mexico be recognized as a taxonomic group and their structural characteristics allow for better understanding of adaptation of species to their environment.

Evolution of flower allometry and pigmentation in Mammillaria haageana (Cactaceae).

BACKGROUND: A puzzle in evolution is the understanding of how the environment might drive subtle phenotypic variation, and whether this variation is adaptive. Under the neutral evolutionary theory, subtle phenotypes are almost neutral with little adaptive value. To test this idea, we studied the infraspecific variation in flower shape and color in Mammillaria haageana, a species with a wide geographical distribution and phenotypic variation, which populations are often recognized as infraspecific taxa. RESULTS: We collected samples from wild populations, kept them in the greenhouse for at least one reproductive year, and collected newly formed flowers. Our first objective was to characterize tepal natural variation in M. haageana through geometric morphometric and multivariate pigmentation analyses. We used landmark-based morphometrics to quantify the trends of shape variation and tepal color-patterns in 20 M. haageana accessions, belonging to five subspecies, plus 8 M. albilanata accessions for comparison as the sister species. We obtained eight geometric morphometric traits for tepal shape and color-patterns. We found broad variation in these traits between accessions belonging to the same subspecies, without taxonomic congruence with those infraspecific units. Also the phenetic cluster analysis showed different grouping patterns among accessions. When we correlated these phenotypes to the environment, we also found that solar radiation might explain the variation in tepal shape and color, suggesting that subtle variation in flower phenotypes might be adaptive. Finally we present anatomical sections in M. haageana subsp. san-angelensis to propose some of the underlying tepal structural features that may give rise to tepal variation. CONCLUSIONS: Our geometric morphometric approach of flower shape and color allowed us to identify the main trends of variation in each accession and putative subspecies, but also allowed us to correlate these variation to the environment, and propose anatomical mechanisms underlying this diversity of flower phenotypes.

Growth Patterns in Seedling Roots of the Pincushion Cactus Mammillaria Reveal Trends of Intra- and Inter-Specific Variation.

Genetic mechanisms controlling root development are well-understood in plant model species, and emerging frontier research is currently dissecting how some of these mechanisms control root development in cacti. Here we show the patterns of root architecture development in a gradient of divergent lineages, from populations to species in Mammillaria. First, we show the patterns of variation in natural variants of the species Mammillaria haageana. Then we compare this variation to closely related species within the Series Supertexta in Mammillaria (diverging for the last 2.1 million years) in which M. haageana is inserted. Finally, we compared these patterns of variation to what is found in a set of Mammillaria species belonging to different Series (diverging for the last 8 million years). When plants were grown in controlled environments, we found that the variation in root architecture observed at the intra-specific level, partially recapitulates the variation observed at the inter-specific level. These phenotypic outcomes at different evolutionary time-scales can be interpreted as macroevolution being the cumulative outcome of microevolutionary phenotypic divergence, such as the one observed in Mammillaria accessions and species.

Blurring the Boundaries between a Branch and a Flower: Potential Developmental Venues in CACTACEAE.

Flowers are defined as short shoots that carry reproductive organs. In Cactaceae, this term acquires another meaning, since the flower is interpreted as a branch with a perianth at the tip, with all reproductive organs embedded within the branch, thus giving way to a structure that has been called a "flower shoot". These organs have long attracted the attention of botanists and cactologists; however, the understanding of the morphogenetic processes during the development of these structures is far from clear. In this review, we present and discuss some classic flower concepts used to define floral structures in Cactaceae in the context of current advances in flower developmental genetics and evolution. Finally, we propose several hypotheses to explain the origin of these floral shoot structures in cacti, and we suggest future research approaches and methods that could be used to fill the gaps in our knowledge regarding the ontogenetic origin of the "flower" in the cactus family.

Evaluating the monophyly of Mammillaria series Supertextae (Cactaceae).

Mammillaria (Cactaceae) taxonomy has been historically problematic due to the morphological variability and sympatry of the species. This has led to several proposals for infrageneric classification, including subgeneric, section and series categories. Mammillaria ser. Supertextae is one of 15 series and is made up of a variable set of species that are mainly distributed in southern Mexico and Central America. However, the phylogenetic relationships within M. ser. Supertextae and its relationship to other Mammillaria taxa are far from fully understood. Here we attempt to elucidate these relationships using complete terminal sampling and newly obtained chloroplast marker sequences and comparing them to Mammillaria species sequences from GenBank. Our phylogenetic analyses showed that M. ser. Supertextae comprises a well-supported monophyletic group that diverged approximately 2.1 Mya and has M. ser. Polyacanthae as its sister group; however, relationships within M. ser. Supertextae remain unresolved. The topology obtained within M. ser. Supertextae must also be interpreted under the distribution shared by these taxa, but it is difficult to differentiate ancestral polymorphisms from possible introgression, given the short time elapsed and the markers used. Our results show that the infrageneric units of M. haageana and M. albilanata can be considered independent evolutionary units. We also suggest that the relationship between M. haageana and M. albilanata is convoluted because their distribution overlaps (mainly towards southern Mexico), with genetic differences that possibly indicate they represent more than two taxonomic entities. One possible explanation is that there could still be gene flow between these taxa, and we might be witnessing an ongoing speciation process.

Does Acid Rain Alter the Leaf Anatomy and Photosynthetic Pigments in Urban Trees?

Megapolis such as Mexico City, have atmospheric pollutants that interact with the humidity and solar radiation. The topography of this city promotes air stagnation, generating atmospheric pollutants and episodes of acid rain, a phenomenon well recorded since the end of the 1980s. However, little we know about how urban trees respond to acid rain in the city. Here we present how simulated acid rain causes anatomical and changes in photosynthetic pigments in two of the most abundant urban trees in Mexico City: Liquidambar styraciflua L. and Fraxinus uhdei (Wenz.) Lingelsh. We first described the leaf anatomy of both species. Then, we used one-year-old trees sprayed with sulfuric acid solutions at pH 2.5 and 3.8, and evaluated visible leaf damage, anatomical alterations, and chlorophyll contents. In both species, the pH 2.5 caused cuticle alterations and areas of total tissue destruction. L. styraciflua showed greater sensitivity, but we discuss some of the tolerance mechanisms. Finally, acid rain also reduced the chlorophyll contents. These results contribute toward a catalogue of urban tree species to describe pollution-induced damages, and the identification of tolerant species useful for short- and mid-term detection of environmental crisis, in cities with similar environmental conditions and urban tree composition.

The barrier function of plant roots: biological bases for selective uptake and avoidance of soil compounds.

The root is the main organ through which water and mineral nutrients enter the plant organism. In addition, root fulfils several other functions. Here, we propose that the root also performs the barrier function, which is essential not only for plant survival but for plant acclimation and adaptation to a constantly changing and heterogeneous soil environment. This function is related to selective uptake and avoidance of some soil compounds at the whole plant level. We review the toolkit of morpho-anatomical, structural, and other components that support this view. The components of the root structure involved in selectivity, permeability or barrier at a cellular, tissue, and organ level and their properties are discussed. In consideration of the arguments supporting barrier function of plant roots, evolutionary aspects of this function are also reviewed. Additionally, natural variation in selective root permeability is discussed which suggests that the barrier function is constantly evolving and is subject of natural selection.

The chloroplast genome of the pincushion cactus Mammilllaria haageana subsp. san-a ngelensis, a Mexican endangered species.

The genus Mammillaria occupies diverse habitats and exhibits diverse growth patterns and a large range of morphologies. Most of the species of this genus are used as ornamental plants and are subject to mass habitat loss. Due to these factors, they are being submitted to selective pressure that might affect conservational efforts and management plans. We obtained the 133 gene chloroplast genome as part of the project of sequencing the complete genome of pincushion cactus, including 88 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The phylogenetic tree indicates the pincushion cactus is a sister species of M. supertexta and M. huitzilopochtli.

Natural Root Cellular Variation in Responses to Osmotic Stress in Arabidopsis thaliana Accessions.

Arabidopsis naturally occurring populations have allowed for the identification of considerable genetic variation remodeled by adaptation to different environments and stress conditions. Water is a key resource that limits plant growth, and its availability is initially sensed by root tissues. The root's ability to adjust its physiology and morphology under water deficit makes this organ a useful model to understand how plants respond to water stress. Here, we used hyperosmotic shock stress treatments in different Arabidopsis accessions to analyze the root cell morphological responses. We found that osmotic stress conditions reduced root growth and root apical meristem (RAM) size, promoting premature cell differentiation without affecting the stem cell niche morphology. This phenotype was accompanied by a cluster of small epidermal and cortex cells with radial expansion and root hairs at the transition to the elongation zone. We also found this radial expansion with root hairs when plants are grown under hypoosmotic conditions. Finally, root growth was less affected by osmotic stress in the Sg-2 accession followed by Ws, Cvi-0, and Col-0; however, after a strong osmotic stress, Sg-2 and Cvi-0 were the most resilience accessions. The sensitivity differences among these accessions were not explained by stress-related gene expression. This work provides new cellular insights on the Arabidopsis root phenotypic variability and plasticity to osmotic stress.

Genome-wide association mapping of date palm fruit traits.

Date palms (Phoenix dactylifera) are an important fruit crop of arid regions of the Middle East and North Africa. Despite its importance, few genomic resources exist for date palms, hampering evolutionary genomic studies of this perennial species. Here we report an improved long-read genome assembly for P. dactylifera that is 772.3 Mb in length, with contig N50 of 897.2 Kb, and use this to perform genome-wide association studies (GWAS) of the sex determining region and 21 fruit traits. We find a fruit color GWAS at the R2R3-MYB transcription factor VIRESCENS gene and identify functional alleles that include a retrotransposon insertion and start codon mutation. We also find a GWAS peak for sugar composition spanning deletion polymorphisms in multiple linked invertase genes. MYB transcription factors and invertase are implicated in fruit color and sugar composition in other crops, demonstrating the importance of parallel evolution in the evolutionary diversification of domesticated species.

A Linear Model to Describe Branching and Allometry in Root Architecture.

Root architecture is a complex structure that comprises multiple traits of the root phenotype. Novel platforms and models have been developed to better understand root architecture. In this methods paper, we introduce a novel allometric model, named rhizochron index (m), which describes lateral root (LR) branching and elongation patterns across the primary root (PR). To test our model, we obtained data from 16 natural accessions of Arabidopsis thaliana at three stages of early root development to measure conventional traits of root architecture (e.g., PR and LR length), and extracted the rhizochron index (m). In addition, we tested previously published datasets to assess the utility of the rhizochron index (m) to distinguish mutants and environmental effects on root architecture. Our results indicate that rhizochron index (m) is useful to distinguish the natural variations of root architecture between A. thaliana accessions, but not across early stages of root development. Correlation analyses in these accessions showed that m is a novel trait that partially captures information from other root architecture traits such as total lateral root length, and the ratio between lateral root and primary root lengths. Moreover, we found that the rhizochron index was useful to distinguish ABA effect on root architecture, as well as the mutant pho1 phenotype. We propose the rhizochron index (m) as a new feature of the root architectural system to be considered, in addition to conventional traits in future investigations.

Redundant and Cryptic Enhancer Activities of the Drosophilayellow Gene.

Cis-regulatory sequences known as enhancers play a key role in regulating gene expression. Evolutionary changes in these DNA sequences contribute to phenotypic evolution. The Drosophilayellow gene, which is required for pigmentation, has emerged as a model system for understanding how cis-regulatory sequences evolve, providing some of the most detailed insights available into how activities of orthologous enhancers have diverged between species. Here, we examine the evolution of yellow cis-regulatory sequences on a broader scale, by comparing the distribution and function of yellow enhancer activities throughout the 5' intergenic and intronic sequences of Drosophila melanogaster, D. pseudoobscura, and D. willistoni We find that cis-regulatory sequences driving expression in a particular tissue are not as modular as previously described, but rather have many redundant and cryptic enhancer activities distributed throughout the regions surveyed. Interestingly, cryptic enhancer activities of sequences from one species often drove patterns of expression observed in other species, suggesting that the frequent evolutionary changes in yellow expression observed among Drosophila species may be facilitated by gaining and losing repression of preexisting cis-regulatory sequences.

The Administration of Cadmium for 2, 3 and 4 Months Causes a Loss of Recognition Memory, Promotes Neuronal Hypotrophy and Apoptosis in the Hippocampus of Rats.

Cadmium (Cd) is a toxic metal and classified as a carcinogen whose exposure could affect the function of the central nervous system. There are studies that suggest that Cd promotes neurodegeneration in different regions of the brain, particularly in the hippocampus. It is proposed that its mechanism of toxicity maybe by an oxidative stress pathway, which modifies neuronal morphology and causes the death of neurons and consequently affecting cognitive tasks. However, this mechanism is not yet clear. The aim of the present work was to study the effect of Cd administration on recognition memory for 2, 3 and 4 months, neuronal morphology and immunoreactivity for caspase-3 and 9 in rat hippocampi. The results show that the administration of Cd decreased recognition memory. Likewise, it caused the dendritic morphology of the CA1, CA3 and dentate gyrus regions of the hippocampus to decrease with respect to the time of administration of this heavy metal. In addition, we observed a reduction in the density of dendritic spines as well as an increase in the immunoreactivity of caspase-3 and 9 in the same hippocampal regions of the animals treated with Cd. These results suggest that Cd affects the structure and function of the neurons of the hippocampus, which contribute to the deterioration of recognition memory. Our results suggest that the exposure to Cd represents a critical health problem, which if not addressed quickly, could cause much more serious problems in the quality of life of the human population, as well as in the environment in which they develop.

The NOAEL Metformin Dose Is Ineffective against Metabolic Disruption Induced by Chronic Cadmium Exposure in Wistar Rats.

Previous studies have proposed that cadmium (Cd) is a metabolic disruptor, which is associated with insulin resistance, metabolic syndrome, and diabetes. This metal is not considered by international agencies for the study of metabolic diseases. In this study, we investigate the effect of metformin on Cd-exposed Wistar rats at a lowest-observed-adverse-effect level (LOAEL) dose (32.5 ppm) in drinking water. Metabolic complications in the rats exposed to Cd were dysglycemia, insulin resistance, dyslipidemia, dyslipoproteinemia, and imbalance in triglyceride and glycogen storage in the liver, muscle, heart, kidney, and adipose tissue. Meanwhile, rats treated orally with a No-observable-adverse-effect level (NOAEL) dose of metformin (200 mg/kg/day) showed mild improvement on serum lipids, but not on glucose tolerance; in tissues, glycogen storage was improved, but lipid storage was ineffective. In conclusion, metformin as a first-line pharmacological therapy must take into consideration the origin and duration of metabolic disruption, because in this work the NOAEL dose of metformin (200 mg/kg/day) showed a limited efficiency in the metabolic disruption caused by chronic Cd exposure.

Fish DNA barcoding around large marine infrastructure for improved biodiversity assessment and monitoring.

Accurate species-level identification is pivotal for environmental assessments and monitoring. The PERU LNG terminal is composed of large marine infrastructure located on the central coast of Peru. Since construction, taxonomically challenging species such as drum fishes (Sciaenidae) have been attracted to the new hard-bottom habitat. We conducted a DNA barcoding study to investigate fish diversity and constructed a DNA barcode reference library. We examined 56 vouchered specimens and identified 24 unique species. Intra- and interspecific divergence estimates ranged between 0 and 0.64% and 11 and 35.5%, respectively. We assessed the efficiency of the reference library to identify 29 non-vouchered specimens. We had 82.5% efficiency by using both our reference library (n = 17) and GenBank (n = 24). We highlight the importance of implementing molecular barcoding for complementing biodiversity assessments in marine environments. This study represents a first step towards generating a comprehensive DNA barcode reference library for marine fishes in Peru.

Towards Providing Solutions to the Air Quality Crisis in the Mexico City Metropolitan Area: Carbon Sequestration by Succulent Species in Green Roofs.

INTRODUCTION: In the first months of 2016, the Mexico City Metropolitan Area experienced the worst air pollution crisis in the last decade, prompting drastic short-term solutions by the Mexico City Government and neighboring States. In order to help further the search for long-term sustainable solutions, we felt obliged to immediately release the results of our research regarding the monitoring of carbon sequestration by green roofs. Large-scale naturation, such as the implementation of green roofs, provides a way to partially mitigate the increased carbon dioxide output in urban areas. METHODS: Here, we quantified the carbon sequestration capabilities of two ornamental succulent plant species, Sedum dendroideum and Sedum rubrotinctum, which require low maintenance, and little or no irrigation. To obtain a detailed picture of these plants' carbon sequestration capabilities, we measured carbon uptake on the Sedum plants by quantifying carbon dioxide exchange and fixation as organic acids, during the day and across the year, on a green roof located in Southern Mexico City. RESULTS: The species displayed their typical CAM photosynthetic metabolism. Moreover, our quantification allowed us to conservatively estimate that a newly planted green roof of Sedum sequesters approximately 180,000,000 ppm of carbon dioxide per year in a green roof of 100 square meters in the short term. DISCUSSION: The patterns of CAM and carbon dioxide sequestration were highly robust to the fluctuations of temperature and precipitation between seasons, and therefore we speculate that carbon sequestration would be comparable in any given year of a newly planted green roof. Older green roof would require regular trimming to mantain their carbon sink properties, but their carbon sequestration capabilities remain to be quantified. Nevertheless, we propose that Sedum green roofs can be part of the long-term solutions to mitigate the air pollution crisis in the Mexico City Metropolitan area, and other "megacities" with marked seasonal drought.

Energy Drink Administration in Combination with Alcohol Causes an Inflammatory Response and Oxidative Stress in the Hippocampus and Temporal Cortex of Rats.

Energy drinks (EDs) are often consumed in combination with alcohol because they reduce the depressant effects of alcohol. However, different researches suggest that chronic use of these psychoactive substances in combination with alcohol can trigger an oxidative and inflammatory response. These processes are regulated by both a reactive astrogliosis and an increase of proinflammatory cytokines such as IL-1ß, TNF-α, and iNOS, causing cell death (apoptosis) at the central and peripheral nervous systems. Currently, mechanisms of toxicity caused by mixing alcohol and ED in the brain are not well known. In this study, we evaluated the effect of chronic alcohol consumption in combination with ED on inflammatory response and oxidative stress in the temporal cortex (TCx) and hippocampus (Hp) of adult rats (90 days old). Our results demonstrated that consuming a mixture of alcohol and ED for 60 days induced an increase in reactive gliosis, IL-1ß, TNF-α, iNOS, reactive oxygen species, lipid peroxidation, and nitric oxide, in the TCx and Hp. We also found immunoreactivity to caspase-3 and a decrease of synaptophysin in the same brain regions. The results suggested that chronic consumption of alcohol in combination with ED causes an inflammatory response and oxidative stress, which induced cell death via apoptosis in the TCx and Hp of the adult rats.

Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop.

Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This analysis documents patterns of post-domestication diversification and provides a genomic resource for this economically important perennial tree crop.