Divergence and reticulation in the Mexican white oaks: ecological and phylogenomic evidence on species limits and phylogenetic networks in the Quercus laeta complex (Fagaceae).

BACKGROUND AND AIMS: Introgressive hybridization poses a challenge to taxonomic and phylogenetic understanding of taxa, particularly when there are high numbers of co-occurring, intercrossable species. The genus Quercus exemplifies this situation. Oaks are highly diverse in sympatry and cross freely, creating syngameons of interfertile species. Although a well-resolved, dated phylogeny is available for the American oak clade, evolutionary relationships within many of the more recently derived clades remain to be defined, particularly for the young and exceptionally diverse Mexican white oak clade. Here, we adopted an approach bridging micro- and macroevolutionary scales to resolve evolutionary relationships in a rapidly diversifying clade endemic to Mexico. METHODS: Ecological data and sequences of 155 low-copy nuclear genes were used to identify distinct lineages within the Quercus laeta complex. Concatenated and coalescent approaches were used to assess the phylogenetic placement of these lineages relative to the Mexican white oak clade. Phylogenetic network methods were applied to evaluate the timing and genomic significance of recent or historical introgression among lineages. KEY RESULTS: The Q. laeta complex comprises six well-supported lineages, each restricted geographically and with mostly divergent climatic niches. Species trees corroborated that the different lineages are more closely related to other species of Mexican white oaks than to each other, suggesting that this complex is polyphyletic. Phylogenetic networks estimated events of ancient introgression that involved the ancestors of three present-day Q. laeta lineages. CONCLUSIONS: The Q. laeta complex is a morphologically and ecologically related group of species rather than a clade. Currently, oak phylogenetics is at a turning point, at which it is necessary to integrate phylogenetics and ecology in broad regional samples to figure out species boundaries. Our study illuminates one of the more complicated of the Mexican white oak groups and lays groundwork for further taxonomic study.

Comparative assessment of water quality indices-a case study to evaluate water quality for drinking water supply and irrigation in Northern Mexico.

Water quality indices (WQIs) are numerical measures used by researchers and water managers to communicate water quality status to the public. This study analyzes the official databases from the CONAGUA monitoring network of the main tributary rivers in the middle basin of the San Pedro-Mezquital River in Durango, Mexico, for a 6-year period (2013-2018). We applied three WQIs to 432 data (18 sampling sites, four samples per year, 6 years): Canadian Council of Ministers of the Environment (CCME) WQI, National Sanitation Foundation (NSF) WQI, and Secretariat of Urban Development and Ecology (SEDUE) WQI. The Canadian index proved to be a flexible, appropriate, and rigorous methodology for assessing water quality based on its use. Results classify the water quality in the studied reservoirs as good, while river water was rated for public use, as marginal to very poor. No statistical significant differences in the quality of water between the rainy (June-October) and dry (November-May) seasons were found. However, tendency shows that in the rainy season the water quality was lower, mainly attributed to agricultural runoffs and bank erosion. The main contamination problem was the presence of fecal coliforms in high concentrations, which is associated to the high population density in the area, low sanitation efficiency, and multiple non-point discharges.

Effect of forest management on tree diversity in temperate ecosystem forests in northern Mexico.

An important challenge for silvicultural practices is the conservation of tree diversity while fulfilling the traditional objectives of forest management, most notably timber harvesting. The purpose of this study was to compare the tree diversity before and after the application of silvicultural treatments in a temperate forest in northern Mexico. Fifteen experimental plots, each measuring 2500 m2, were established to evaluate the immediate effect of four silvicultural treatments. These treatments were identified by their levels of management: intensive (clearcut, removal 100%), semi-intensive (removal of 59-61% of basal area), conservative (removal of 29-31% of basal area), and a control group. New forest guidelines, in contrast to conventional approaches, were applied to the semi-intensive and conservative treatments based on health and diversity conditions. Basal area, canopy cover, tree and total volume were measured in each plot. The Importance Value Index, alpha diversity, and evenness were estimated before and after treatments. Eighteen species belonging to five genera and five families were found in the study area. The species with the highest ecological values were Pinus durangensis, P. teocote, Quercus sideroxyla, and Quercus convallata with IVI numbers between 13.6 and 24.5%. Alpha diversity was intermediate (Margalef: 2.9 to 3.8), while dominance and evenness were above average compared to other studies (Simpson: 0.69 to 0.77; Shannon-Wiener: 1.44 to 1.6; Pielou: 0.76 to 0.85). The species evenness index in the conservative treatment was high (Sorensen, Jaccard, quantitative Sorensen and Morisita-Horn; 88 to 99%), although abundance decreased. Overall, there were no significant differences in IVI values and diversity indicators before and after treatments, with the exception of the clearcut treatment. When associating the diversity indices with stand variables, only the Pielou's evenness index showed a significant relationship between them. We concluded that both the conservative and semi-intensive treatments did not generate significant changes in tree diversity, but the former had slightly higher alpha diversity indices. These results can provide a better insight on silvicultural practices and their effects on species composition.

Tall Pinus luzmariae trees with genes from P. herrerae.

CONTEXT: Pinus herrerae and P. luzmariae are endemic to western Mexico, where they cover an area of more than 1 million hectares. Pinus herrerae is also cultivated in field trials in South Africa and South America, because of its considerable economic importance as a source of timber and resin. Seed quality, afforestation success and desirable traits may all be influenced by the presence of hybrid trees in seed stands. AIMS: We aimed to determine the degree of hybridization between P. herrerae and P. luzmariae in seed stands of each species located in the Sierra Madre Occidental, Durango, Mexico. METHODS: AFLP molecular markers from samples of 171 trees across five populations were analyzed with STRUCTURE and NewHybrids software to determine the degree of introgressive hybridization. The accuracy of STRUCTURE and NewHybrids in detecting hybrids was quantified using the software Hybridlab 1.0. Morphological analysis of 131 samples from two populations of P. herrerae and two populations of P. luzmariae was also conducted by Random Forest classification. The data were compared by Principal Coordinate Analysis (PCoA) in GenAlex 6.501. RESULTS: Hybridization between Pinus herrerae and P. luzmariae was observed in all seed stands under study and resulted in enhancement of desirable silvicultural traits in the latter species. In P. luzmariae, only about 16% molecularly detected hybrids correspond to those identified on a morphological basis. However, the morphology of P. herrerae is not consistent with the molecularly identified hybrids from one population and is only consistent with 3.3 of those from the other population. CONCLUSIONS: This is the first report of hybrid vigour (heterosis) in Mexican pines. Information about hybridization and introgression is essential for developing effective future breeding programs, successful establishment of plantations and management of natural forest stands. Understanding how natural hybridization may influence the evolution and adaptation of pines to climate change is a cornerstone to sustainable forest management including adaptive silviculture.

Genomic landscape of the global oak phylogeny.

The tree of life is highly reticulate, with the history of population divergence emerging from populations of gene phylogenies that reflect histories of introgression, lineage sorting and divergence. In this study, we investigate global patterns of oak diversity and test the hypothesis that there are regions of the oak genome that are broadly informative about phylogeny. We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing nearly 250 Quercus species to infer a time-calibrated phylogeny of the world's oaks. We use a reversible-jump Markov chain Monte Carlo method to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20 000 RAD-seq loci back to an annotated oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny. Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification, probably in response to climatic transitions or ecological opportunity. The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.

Distribución potencial de dos subespecies de Montanoa tomentosa (Asteracerae) en México / Potential distribution of two subspecies of Montanoa tomentosa (Asteracerae) in Mexico

Introducción: la Montanoa tomentosa es un recurso fitogenético con propiedades medicinales utilizado en México. A pesar de su relevancia botánica, la información específica de las distribuciones de taxones infraespecíficos y la los factores que influyen en su desarrollo aún son limitados. Objetivo: Informar el potencial geográfico distribución y las variables ambientales asociadas a nichos ecológicos de dos subespecies de M. tomentosa (M. tomentosa subsp. Tomentosa y M. tomentosa subsp. Xanthiifolia) en territorio mexicano. Métodos: A Se creó una base de datos de registros de herbario, se realizó una búsqueda sistemática in situ de ambas subespecies desde Octubre de 2015 a marzo de 2016, durante la temporada de floración y fructificación. Posteriormente, recorridos exploratorios (Guanajuato, Querétaro, Hidalgo, Ciudad de México, Estado de México, Puebla, Oaxaca y Chiapas). Un total de 181 Se muestrearon y georreferenciaron individuos, generando nuevos registros para la actualización de la base de datos. Tres hábitat modelos de idoneidad (complejo M. tomentosa, M. tomentosa subsp. tomentosa y M. tomentosa subsp. xanthiifolia) se generaron utilizando el software MaxEnt. Este software estima la probabilidad de distribución de especies. utilizando datos georreferenciados y características ambientales como predictores, mediante el logaritmo de entropía máxima y el método bayesiano. Resultados: De 22 variables ambientales utilizadas como predictores, cinco (estacionalidad de temperatura, isotermalidad, temperatura máxima del mes más cálido, precipitación del más cálido trimestre y precipitación del trimestre más húmedo) contribuyeron con el 70,2% de la contribución porcentual total. los El modelo mostró una distribución potencial de 77 688 km2, aproximadamente el 4% del territorio de la República Mexicana. Ambos La subespecie creció entre 500 y 2 500 m. Se asociaron a vegetación xerófila y heliófila, a veces también estaban ubicadas en la periferia o incrustadas en aberturas de bosques templados y subhúmedos. No estuvieron presentes regiones secas del norte del país. Conclusiones: estacionalidad de la temperatura, isotermalidad y la temperatura máxima del mes más cálido determinan la distribución de la especie. Precipitación del cuarto más cálido y la precipitación del cuarto más húmedo define el hábitat entre M. tomentosa subsp. tomentosa y M. tomentosa subsp. xanthiifolia. Estos hallazgos aclaran las preferencias ecológicas y la delimitación los taxones infraespecíficos de M. tomentosa.

Introduction: Montanoa tomentosa is a phytogenetic resource with medicinal properties used in Mexico. Despite its botanic relevance, the specific information of infraespecific taxa distributions and the environmental factors that influence their development is still limited. Objective: To report the potential geographic distribution and the environmental variables associated to ecological niches of two subspecies of M. tomentosa (M. tomentosa subsp. tomentosa and M. tomentosa subsp. xanthiifolia) in the Mexican territory. Methods: A database of herbarium records was created, an in situ systematic search of both subspecies was carried out from October 2015 to March 2016, during the flowering-fruiting season. After that, exploratory tours (Guanajuato, Querétaro, Hidalgo, Mexico City, State of Mexico, Puebla, Oaxaca and Chiapas) were realized. A total of 181 individuals were sampled and georeferenced, generating new records for the database upgrading. Three habitat suitability models (M. tomentosa complex, M. tomentosa subsp. tomentosa and M. tomentosa subsp. xanthiifolia) were generated using the MaxEnt software. These software estimates the probability of species distribution using geo-referenced data and environmental characteristics as predictors, through the maximum entropy logarithm and the Bayesian method. Results: From 22 environmental variables used as predictors, five (seasonality of temperature, isothermality, maximum temperature of the warmest month, precipitation of the warmest trimester and precipitation of the wettest trimester) contributed 70.2 % of the total percentage contribution. The model showed a potential distribution of 77 688 km2, approximately 4 % of the Mexican Republic territory. Both subspecies grew between 500 and 2 500 m. They were associated to xerophilous and heliophiles vegetation, sometimes they were located in the periphery or embed in openings of temperate and sub-humid forests too. They were not present dry regions from the North of the country. Conclusions: Temperature seasonality, isothermality and maximum temperature of the warmest month determine the distribution of the species. Precipitation of the warmest quarter and precipitation of wettest quarter defines the habitat between M. tomentosa subsp. tomentosa and M. tomentosa subsp. xanthiifolia. These findings clarify the ecological preferences and delimitation the infraspecific taxa of M. tomentosa.

Analysis of retrotransposon abundance, diversity and distribution in holocentric Eleocharis (Cyperaceae) genomes.

Background and Aims: Long terminal repeat-retrotransposons (LTR-RTs) comprise a large portion of plant genomes, with massive repeat blocks distributed across the chromosomes. Eleocharis species have holocentric chromosomes, and show a positive correlation between chromosome numbers and the amount of nuclear DNA. To evaluate the role of LTR-RTs in karyotype diversity in members of Eleocharis (subgenus Eleocharis), the occurrence and location of different members of the Copia and Gypsy superfamilies were compared, covering interspecific variations in ploidy levels (considering chromosome numbers), DNA C-values and chromosomal arrangements. Methods: The DNA C-value was estimated by flow cytometry. Genomes of Eleocharis elegans and E. geniculata were partially sequenced using Illumina MiSeq assemblies, which were a source for searching for conserved proteins of LTR-RTs. POL domains were used for recognition, comparing families and for probe production, considering different families of Copia and Gypsy superfamilies. Probes were obtained by PCR and used in fluorescence in situ hybridization (FISH) against chromosomes of seven Eleocharis species. Key Results: A positive correlation between ploidy levels and the amount of nuclear DNA was observed, but with significant variations between samples with the same ploidy levels, associated with repetitive DNA fractions. LTR-RTs were abundant in E. elegans and E. geniculata genomes, with a predominance of Copia Sirevirus and Gypsy Athila/Tat clades. FISH using LTR-RT probes exhibited scattered and clustered signals, but with differences in the chromosomal locations of Copia and Gypsy. The diversity in LTR-RT locations suggests that there is no typical chromosomal distribution pattern for retrotransposons in holocentric chromosomes, except the CRM family with signals distributed along chromatids. Conclusions: These data indicate independent fates for each LTR-RT family, including accumulation between and within chromosomes and genomes. Differential activity and small changes in LTR-RTs suggest a secondary role in nuclear DNA variation, when compared with ploidy changes.

The role of hybridization during ecological divergence of southwestern white pine (Pinus strobiformis) and limber pine (P. flexilis).

Interactions between extrinsic factors, such as disruptive selection and intrinsic factors, such as genetic incompatibilities among loci, often contribute to the maintenance of species boundaries. The relative roles of these factors in the establishment of reproductive isolation can be examined using species pairs characterized by gene flow throughout their divergence history. We investigated the process of speciation and the maintenance of species boundaries between Pinus strobiformis and Pinus flexilis. Utilizing ecological niche modelling, demographic modelling and genomic cline analyses, we illustrated a divergence history with continuous gene flow. Our results supported an abundance of advanced generation hybrids and a lack of loci exhibiting steep transition in allele frequency across the hybrid zone. Additionally, we found evidence for climate-associated variation in the hybrid index and niche divergence between parental species and the hybrid zone. These results are consistent with extrinsic factors, such as climate, being an important isolating mechanism. A build-up of intrinsic incompatibilities and of coadapted gene complexes is also apparent, although these appear to be in the earliest stages of development. This supports previous work in coniferous species demonstrating the importance of extrinsic factors in facilitating speciation. Overall, our findings lend support to the hypothesis that varying strength and direction of selection pressures across the long lifespans of conifers, in combination with their other life history traits, delays the evolution of strong intrinsic incompatibilities.

Phenolic constituents and antioxidant properties of five wild species of Physalis (Solanaceae).

BACKGROUND: Fruits of wild species of the genus Physalis are consumed as food and calyces and leaves are used in traditional medicine. The phenolic composition of the species of this genus have been scarcely studied. To contribute to a better knowledge for the use of all the potential of these wild species of plants, leaves, fruits, and calyces of five wild species of the genus were analyzed for their phenolic composition and antioxidant properties. RESULTS: Important tissue- and species-dependent variations were found. Calyces of Physalis subulata showed the highest contents of phenolics (176.58 mg of gallic acid equivalents/g dry tissue), flavonoids (39.63 mg/g dry tissue), and phenolic acids (50.57 mg of quercitrin equivalents/g dry tissue), and its leaves displayed the highest total antioxidant capacity (3.59 mg of ascorbic acid equivalents/mL) and one of the highest reduction powers (0.54 µg of ascorbic acid equivalents/mL). A high performance liquid chromatography with photodiode array detection analysis revealed a total of 28 phenolic compounds in foliar tissues (mainly kaempferol-3-O-glycosides), 16 in fruits (mainly phenolic acids), and 16 in calyces (mainly kaempferol-3-O-glycosides); the profiles of these compounds in the three types of tissue were species-specific. CONCLUSIONS: The studied species of Physalis are important sources of phenolics with relevant antioxidant activity. The current results indicate that phenolic profiles are valuable specific chemical markers and can be relevant as food tracing and authenticity indicators for plant-based preparations involving species of Physalis.