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      Estructura genética poblacional de la lagartija arenera Uma exsul Schmidt y Bogert, 1947, en el desierto Chihuahuense Translated title: Population genetic structure of the sand lizard, Uma exsul Schmidt and Bogert, 1947, in the Chihuahuan desert

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          Abstract

          Resumen Uma exsul es una especie microendémica del desierto Chihuahuense, se encuentra enlistada en la NOM-059-SEMARNAT-2010 como en peligro de extinción. El objetivo fue determinar la estructura genética poblacional de U. exsul, suponiendo que las poblaciones con distribución alopátrica, constituyen linajes distintos. Metodología: se realizaron 14 salidas al campo y se colectaron un total de 24 muestras biológicas. Se utilizó el gen Citocromo b para el análisis BAPS. Para determinar el patrón de haplotipos se utilizó el programa TCS. Se calculó la D de Tajima para determinar la selección o deriva de las poblaciones y una AMOVA para determinar la Fst y el flujo genético poblacional. Se registró una baja selección (Tajima D = 0.000, p ≤ 0.001) . La variación genética interpoblacional de 12.91% es baja, la intrapoblacional es alta (87.09 %), con Fst: 0.13113 y Nm: 3.31 (p < 0.001). Existe incipiente estructura con una población en evolución sin selección y alto flujo genético interpoblacional en Viesca; Estación Marte tuvo un barrido selectivo reciente y posterior expansión de la población después de un cuello de botella reciente. Se concluye que las muestras conforman tres grupos genéticos, indicando que la población Estación Marte se le puede considerar como una población alopátrica.

          Translated abstract

          Abstract Uma exsul is a micro-endemic species of the Chihuahuan desert, listed as an endangered species in NOM-059-SEMARNAT-2010. The objective was to determine the genetic population structure of U. exsul, assuming that the distribution allopatric populations constitute different lineages. Methodology: 14 field trips where carried out, collecting 24 biological samples. Cytochrome b was used for BAPS analysis. The TCS program was used to determine the haplotype pattern. We calculated Tajima’s D to determine the selection or drift of populations and an AMOVA to determine the Fst and the population gene flow. A low selection was recorded (Tajima’s D = 0.000, p ≤ 0. 001). The AMOVA interpopulation 12.91% is low, the intrapopulation is high (87.09%), with Fst: 0.13113 and Nm: 3.31 (p < 0.001). There is an incipient structure with an evolving population without selection and high interpopulational genetic flow in Viesca; Estación Marte had a recent selective sweep and subsequent population expansion after a recent bottleneck. We conclude that the samples make up three genetic groups, considering the Estación Marte population as an allopatric population.

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          A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation.

          We previously developed a cladistic approach to identify subsets of haplotypes defined by restriction endonuclease mapping or DNA sequencing that are associated with significant phenotypic deviations. Our approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site or sequence data that represents the evolutionary steps that interrelate the observed haplotypes. The cladogram is used to define a nested statistical design to identify mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that any undetected mutation causing a phenotypic effect is embedded within the same evolutionary history that is represented by the cladogram. The power of this approach depends upon the confidence one has in the particular cladogram used to draw inferences. In this paper, we present a strategy for estimating the set of cladograms that are consistent with a particular sample of either restriction site or nucleotide sequence data and that includes the possibility of recombination. We first evaluate the limits of parsimony in constructing cladograms. Once these limits have been determined, we construct the set of parsimonious and nonparsimonious cladograms that is consistent with these limits. Our estimation procedure also identifies haplotypes that are candidates for being products of recombination. If recombination is extensive, our algorithm subdivides the DNA region into two or more subsections, each having little or no internal recombination. We apply this estimation procedure to three data sets to illustrate varying degrees of cladogram ambiguity and recombination.
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            Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers.

            With a standard set of primers directed toward conserved regions, we have used the polymerase chain reaction to amplify homologous segments of mtDNA from more than 100 animal species, including mammals, birds, amphibians, fishes, and some invertebrates. Amplification and direct sequencing were possible using unpurified mtDNA from nanogram samples of fresh specimens and microgram amounts of tissues preserved for months in alcohol or decades in the dry state. The bird and fish sequences evolve with the same strong bias toward transitions that holds for mammals. However, because the light strand of birds is deficient in thymine, thymine to cytosine transitions are less common than in other taxa. Amino acid replacement in a segment of the cytochrome b gene is faster in mammals and birds than in fishes and the pattern of replacements fits the structural hypothesis for cytochrome b. The unexpectedly wide taxonomic utility of these primers offers opportunities for phylogenetic and population research.
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              Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software

              Phylogeographical analyses have become commonplace for a myriad of organisms with the advent of cheap DNA sequencing technologies. Bayesian model-based clustering is a powerful tool for detecting important patterns in such data and can be used to decipher even quite subtle signals of systematic differences in molecular variation. Here, we introduce two upgrades to the Bayesian Analysis of Population Structure (BAPS) software, which enable 1) spatially explicit modeling of variation in DNA sequences and 2) hierarchical clustering of DNA sequence data to reveal nested genetic population structures. We provide a direct interface to map the results from spatial clustering with Google Maps using the portal http://www.spatialepidemiology.net/ and illustrate this approach using sequence data from Borrelia burgdorferi. The usefulness of hierarchical clustering is demonstrated through an analysis of the metapopulation structure within a bacterial population experiencing a high level of local horizontal gene transfer. The tools that are introduced are freely available at http://www.helsinki.fi/bsg/software/BAPS/.
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                Author and article information

                Journal
                biotecnia
                Biotecnia
                Biotecnia
                Universidad de Sonora, División de Ciencias Biológicas y de la Salud (Hermosillo, Sonora, Mexico )
                1665-1456
                2020
                : 22
                : 1
                : 102-108
                Affiliations
                [3] Michoacán orgnameInstituto de Ecología A.C. Mexico
                [2] orgnameUniversidad Autónoma de Nuevo León orgdiv1Facultad de Ciencias Biológicas Mexico
                [1] Durango orgnameUniversidad Juárez del Estado de Durango orgdiv1Facultad de Ciencias Biológicas
                Article
                S1665-14562020000100102 S1665-1456(20)02200100102
                10.18633/biotecnia.v22i1.1156
                5ffedee1-2109-412a-adc4-2ca779fbfcda

                This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

                History
                : 20 May 2019
                : 27 November 2018
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 37, Pages: 7
                Product

                SciELO Mexico

                Categories
                Artículos

                haplotipos,lagartija de arena,haplotypes,genetic group,allopatry,genetic structure,Fringe-toed lizard,alopátrica,estructura genética,grupos genéticos

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