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When conservation genetics is used to decipher the evolutionary relationships among species, DNA sequence comparisons are often made. Sequencing a region of a gene and properly analyzing the data may lead to novel findings. Based on analyzing underlying genetic variation, there could be evidence to suggest that a revision of numbers of species might be warranted. What was once considered a single species with two populations, for example, might actually merit consideration for separate species status. The level of genetic differentiation detected could have significant implications for how they are protected in the wild and the measures that must be taken by local, state, and federal authorities. Alternatively, the data may indicate that these populations are not sufficiently genetically different to merit separate species designations. DNA sequences are also used to aid in diagnosing natural units for conservation in the wild. Detecting fixed nucleotide characters among DNA sequences between well-sampled populations can provide sufficient evidence for defining units of conservation that potentially merit separate species status under the Phylogenetic Species Concept. Several studies have used DNA sequence polymorphism shared by certain units to the exclusion of other groups to unequivocally define or diagnose species.

Population-level analyses use DNA sequences as well as another set of molecular markers, called microsatellites, a type of repetitive DNA element. Microsatellites are used to address many conservation genetics questions. They are short, tandem-repeated motifs of DNA sequences, such as a di-nucleotide repeat (e.g., (AT)n), that usually vary in the number of repeats in a particular stretch of DNA. They are distributed throughout the genomes of plants and animals, are inherited in a Mendelian fashion, and have been polymorphic occurring found to be highly polymorphic. These genetic markers have proven to be useful in population studies for such purposes as estimating gene flow between populations, describing the genetic variation within and between populations, and examining the effects of hybridization between species. They are used in pedigree analysis to identify individuals based on a DNA sample, and they are used to decipher mating strategies and degrees of relat-edness among members of a population.

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