Diversity across Seasons of Culturable Pseudomonas from a Desiccation Lagoon in Cuatro Cienegas, Mexico.

Cuatro Cienegas basin (CCB) is a biodiversity reservoir within the Chihuahuan desert that includes several water systems subject to marked seasonality. While several studies have focused on biodiversity inventories, this is the first study that describes seasonal changes in diversity within the basin. We sampled Pseudomonas populations from a seasonally variable water system at four different sampling dates (August 2003, January 2004, January 2005, and August 2005). A total of 70 Pseudomonas isolates across seasons were obtained, genotyped by fingerprinting (BOX-PCR), and taxonomically characterized by 16S rDNA sequencing. We found 35 unique genotypes, and two numerically dominant lineages (16S rDNA sequences) that made up 64% of the sample: P. cuatrocienegasensis and P. otitidis. We did not recover genotypes across seasons, but lineages reoccurred across seasons; P. cuatrocienegasensis was isolated exclusively in winter, while P. otitidis was only recovered in summer. We statistically show that taxonomic identity of isolates is not independent of the sampling season, and that winter and summer populations are different. In addition to the genetic description of populations, we show exploratory measures of growth rates at different temperatures, suggesting physiological differences between populations. Altogether, the results indicate seasonal changes in diversity of free-living aquatic Pseudomonas populations from CCB

Understanding the Evolutionary Relationships and Major Traits of \u3cem\u3eBacillus\u3c/em\u3e through Comparative Genomics

Background: The presence of Bacillus in very diverse environments reflects the versatile metabolic capabilities of a widely distributed genus. Traditional phylogenetic analysis based on limited gene sampling is not adequate for resolving the genus evolutionary relationships. By distinguishing between core and pan-genome, we determined the evolutionary and functional relationships of known Bacillus. Results: Our analysis is based upon twenty complete and draft Bacillus genomes, including a newly sequenced Bacillus isolate from an aquatic environment that we report for the first time here. Using a core genome, we were able to determine the phylogeny of known Bacilli, including aquatic strains whose position in the phylogenetic tree could not be unambiguously determined in the past. Using the pan-genome from the sequenced Bacillus, we identified functional differences, such as carbohydrate utilization and genes involved in signal transduction, which distinguished the taxonomic groups. We also assessed the genetic architecture of the defining traits of Bacillus, such as sporulation and competence, and showed that less than one third of the B. subtilis genes are conserved across other Bacilli. Most variation was shown to occur in genes that are needed to respond to environmental cues, suggesting that Bacilli have genetically specialized to allow for the occupation of diverse habitats and niches. Conclusions: The aquatic Bacilli are defined here for the first time as a group through the phylogenetic analysis of 814 genes that comprise the core genome. Our data distinguished between genomic components, especially core vs. pan-genome to provide insight into phylogeny and function that would otherwise be difficult to achieve. A phylogeny may mask the diversity of functions, which we tried to uncover in our approach. The diversity of sporulation and competence genes across the Bacilli was unexpected based on previous studies of the B. subtilis model alone. The challenge of uncovering the novelties and variations among genes of the non-subtilis groups still remains. This task will be best accomplished by directing efforts toward understanding phylogenetic groups with similar ecological niches

Molecular phylogeny of Mexican species of freshwater prawn genus Macrobrachium (Decapoda: Palaemonidae: Palaemoninae)

Molecular phylogenetic analyses of 16 species of the freshwater prawn genus Macrobrachium from Mexico are presented. The phylogenetic reconstructions are based on partial sequences from16S rDNA mitochondrial gene. The results show a clear separation of the species with extended larval development (ED) from those with abbreviated larval development (AD). Within the ED clade, the species of the Olfersii Group clustered together, which is in agreement with their morphological similarity, whereas the position of the three pairs of geminate species within this clade suggests different origins. Five Mexican species are grouped into a single clade suggesting a common origin in a species with few larval stages and relatively large eggs. The estimated time of evolutionary divergence suggests that the ED and AD clades diverged in the Middle Eocene; the three geminate pairs differentiated at different times, and the species of the AD group originated during the Early Pliocene

Do the Historical Biogeography and Evolutionary History of the Digenean Margotrema spp. across Central Mexico Mirror Those of Their Freshwater Fish Hosts (Goodeinae)?

Host-parasite systems provide an ideal platform to study evolution at different levels, including codivergence in a historical biogeography context. In this study we aim to describe biogeographic and codivergent patterns and associated processes of the Goodeinae freshwater fish and their digenean parasite (Margotrema spp.) over the last 6.5 Ma (million years), identifying the main factors (host and/or hydrogeomorphology) that influenced the evolution of Margotrema. We obtained a species tree for Margotrema spp. using DNA sequence data from mitochondrial and nuclear molecular markers (COI and ITS1, respectively) and performed molecular dating to discern divergence events within the genus. The dispersal-extinction-cladogenesis (DEC) model was used to describe the historical biogeography of digeneans and applied to cophylogenetic analyses of Margotrema and their goodeine hosts. Our results showed that the evolutionary history of Margotrema has been shaped in close association with its geographic context, especially with the geological history of central Mexico during the Pleistocene. Host-specificity has been established at three levels of historical association: a) Species-Species, represented by Xenotaenia resolanae -M. resolanae exclusively found in the Cuzalapa River Basin; b) Species-Lineage, represented by Characodon audax-M. bravoae Lineage II, exclusive to the Upper and Middle Mezquital River Basin, and c) Tribe-Lineage, including two instances of historical associations among parasites and hosts at the taxonomical level of tribe, one represented by Ilyodontini-M. bravoae Lineage I (distributed across the Ayuquila and Balsas River Basins), and another comprised of Girardinichthyini/Chapalichthyini-M. bravoae Lineage III, found only in the Lerma River Basin. We show that the evolutionary history of the parasites is, on several occasions, in agreement with the phylogenetic and biogeographic history of their hosts. A series of biogeographic and host-parasite events explain the codivergence patterns observed, in which cospeciation and colonisation via host-switching and vicariant plus dispersal events are appreciated, at different times during the diversification history of both associates, particularly during the Pleistocene.Facultad de Ciencias Naturales y Muse

High diversity and suggested endemicity of culturable Actinobacteria in an extremely oligotrophic desert oasis

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

Parámetros, correlaciones y tendencias genéticas de caracteres reproductivos en ganado Holstein de México

The objective was to calculate the parameters, correlations and describe the genetic trends of reproductive traits in Holstein cattle from Mexico in three different periods of time, in females born between 2006 and 2019, using records of the Mexican Holstein association. The reproductive parameters calculated were: calving to first insemination interval (CFI), number of services per conception (NSC), days open (DO), interval between calving (IBC), and age at first calving (AFC). The components of variance were estimated using restricted maximum likelihood in an animal model, to calculate genetic parameters (narrow-sense heritability (h2), repeatability (r) and genetic correlations) and phenotypic correlations. Additive genetic variances and genetic values were also estimated in three periods of time (P1: 2006-2009, P2: 2010-2013 and P3: 2014-2017). The calculated heritabilities were from 4 to 9 % and the repeatabilities from 8 to 9 %, values close to previous reports for fertility traits. Phenotypic correlations were positive for almost all reproductive parameters and genetic correlations were positive over a wide range (0.13-0.99). Analyses by period showed changes, possibly derived from the influence of the import and use of germplasm from foreign bulls (mainly from the United States of America and Canada) which implement genomic selection and include fertility traits. The present research has made it possible to update the information on reproductive and genetic parameters in fertility traits that can be incorporated into national genetic evaluations.El objetivo fue calcular los parámetros, correlaciones y describir las tendencias genéticas de caracteres reproductivos en ganado Holstein de México en tres periodos diferentes de tiempo, en hembras nacidas entre 2006 y 2019, usando registros de la asociación Holstein de México. Los parámetros reproductivos calculados fueron: intervalo parto a primer servicio (IPPS), el número de servicios por concepción (NSC), los días abiertos (DAB), el intervalo entre partos (IEP) y la edad al primer parto (EPP). Los componentes de la varianza fueron estimados utilizando máxima verosimilitud restringida en un modelo animal, para calcular parámetros genéticos (heredabilidad en sentido estricto (h2), repetibilidad (r) y correlaciones genéticas) y correlaciones fenotípicas. También se estimaron varianzas genéticas aditivas y valores genéticos en tres periodos de tiempo (P1: 2006-2009, P2: 2010-2013 y P3: 2014-2017). Las heredabilidades calculadas fueron de 4 a 9 % y las repetibilidades del 8 al 9 %, valores cercanos a reportes previos para características de fertilidad. Las correlaciones fenotípicas fueron positivas para casi todos los parámetros reproductivos y las genéticas fueron positivas en un rango amplio (0.13-0.99). Los análisis por periodos mostraron cambios, posiblemente derivados de la influencia de la importación y uso de germoplasma de toros extranjeros (principalmente de los Estados Unido de América y Canadá) que implementan selección genómica e incluyen características fertilidad. La presente investigación ha permitido actualizar la información de parámetros reproductivos y genéticos en caracteres de fertilidad que podrán ser incorporados a las evaluaciones genéticas nacionales

Genomic lineages of Rhizobium etli revealed by the extent of nucleotide polymorphisms and low recombination

<p>Abstract</p> <p>Background</p> <p>Most of the DNA variations found in bacterial species are in the form of single nucleotide polymorphisms (SNPs), but there is some debate regarding how much of this variation comes from mutation versus recombination. The nitrogen-fixing symbiotic bacteria <it>Rhizobium etli </it>is highly variable in both genomic structure and gene content. However, no previous report has provided a detailed genomic analysis of this variation at nucleotide level or the role of recombination in generating diversity in this bacterium. Here, we compared draft genomic sequences versus complete genomic sequences to obtain reliable measures of genetic diversity and then estimated the role of recombination in the generation of genomic diversity among <it>Rhizobium etli</it>.</p> <p>Results</p> <p>We identified high levels of DNA polymorphism in <it>R. etli</it>, and found that there was an average divergence of 4% to 6% among the tested strain pairs. DNA recombination events were estimated to affect 3% to 10% of the genomic sample analyzed. In most instances, the nucleotide diversity (π) was greater in DNA segments with recombinant events than in non-recombinant segments. However, this degree of recombination was not sufficiently large to disrupt the congruence of the phylogenetic trees, and further evaluation of recombination in strains quartets indicated that the recombination levels in this species are proportionally low.</p> <p>Conclusion</p> <p>Our data suggest that <it>R. etli </it>is a species composed of separated lineages with low homologous recombination among the strains. Horizontal gene transfer, particularly via the symbiotic plasmid characteristic of this species, seems to play an important role in diversity but the lineages maintain their evolutionary cohesiveness.</p

Genomic variation in recently collected maize landraces from Mexico

AbstractThe 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