Restriction site‐associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference
- A. Mastretta‐Yanes, N. Arrigo, N. Alvarez, T. H. Jorgensen, D. Piñero, B. Emerson
- BiologyMolecular Ecology Resources
- 1 January 2015
Individual sample replicates are used, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome and optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci.
Phylogenetics of Pinus (Pinaceae) based on nuclear ribosomal DNA internal transcribed spacer region sequences.
- A. Liston, W. Robinson, D. Piñero, E. Álvarez-Buylla
- BiologyMolecular Phylogenetics and Evolution
- 1 February 1999
A 650-bp portion of the nuclear ribosomal DNA internal transcribed spacer region was sequenced in 47 species of Pinus, representing all recognized subsections of the genus, and 2 species of Picea and Cathaya as outgroups, highlighting taxa of particularly problematic placement including Pinus nelsonii and P. aristata.
Variation in the nrDNA ITS of Pinus subsection Cembroides: implications for molecular systematic studies of pine species complexes.
Within the pinyon clade, phylogenetic structure is present, but different clones from the same (or different) individuals of a species are polyphyletic, indicating that coalescence of ITS copies within individual genomes predates evolutionary divergence in the group.
Genetic structure, outcrossing rate and heterosis in Astrocaryum mexicanum (tropical palm): implications for evolution and conservation
The population genetics of the understory tropical rain forest palm Astrocaryum mexicanum were studied in Los Tuxtlas, Veracruz, Mexico, using enzyme electrophoresis and appear not to satisfy the conditions necessary for non-adaptive evolution, a hypothesis commonly invoked to explain high tropical tree diversity.
High population differentiation and genetic variation in the endangered Mexican pine Pinus Rzedowskii (Pinaceae).
- P. Delgado, D. Piñero, Á. Chaos, N. Pérez-Nasser, E. Álvarez-Buylla
- BiologyAmerican-Eurasian journal of botany
- 1 May 1999
A convex relationship between the genetic distance among populations and the number of ancestral lineages is found, suggesting that demographically this species has not been at risk recently.
Genetic structure of a soil population of nonsymbiotic Rhizobium leguminosarum
- L. Segovia, D. Piñero, R. Palacios, E. Martínez-Romero
- BiologyApplied and Environmental Microbiology
- 1 February 1991
The genetic structure of a population of nonsymbiotic Rhizobium leguminosarum strains was determined by the electrophoretic mobilities of eight metabolic enzymes by finding the rRNA operon restriction fragment length polymorphisms and the nucleotide sequence of a fragment of the 16S rRNA gene were identical to those of R. leguminOSarum bv.
Hierarchical analysis of linkage disequilibrium in Rhizobium populations: evidence for sex?
- V. Souza, T. T. Nguyen, R. Hudson, D. Piñero, R. Lenski
- BiologyProceedings of the National Academy of Sciences…
- 1 September 1992
The genetic structure of Rhizobium leguminosarum biovar phaseoli populations associated with wild and cultivated beans (Phaseolus spp.) over several spatial scales, ranging from individual host plants to throughout the Western Hemisphere, suggests that limited migration between populations contributes substantially to linkage disequilibrium.
Ancestry and divergence of subtropical montane forest isolates: molecular biogeography of the genus Abies (Pinaceae) in southern México and Guatemala
Trends suggest that the Mesoamerican Abies share a recent common ancestor and that their divergence and speciation is mainly driven by genetic drift and isolation during the warm interglacial periods.
Genetic Structure of Rhizobium etli biovar phaseoli Associated with Wild and Cultivated Bean Plants (Phaseolus vulgaris and Phaseolus coccineus) in Morelos, Mexico
The analysis of the genetic structure of Rhizobium strains may allow the identification of strains that are naturally well adapted to a wide range of different environments, which may be useful for agricultural purposes or as a starting point for developing improved RhizOBium strains.
Genetic diversity and relationships among isolates of Rhizobium leguminosarum biovar phaseoli
Fifty-one isolates of Rhizobium leguminosarum biovar phaseoli from various geographic and ecological sources, largely in Mexico, were characterized by the electrophoretic mobilities of 15 metabolic…