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Ecological and genetic studies of the sand skink (Plestiodon reynoldsi) in central and south Florida/Research to Benefit the conservation of the Florida Sand Skink

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  • Swaim Biological Inc.
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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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Thesis (M.S.)--University of South Florida, 2001. Includes bibliographical references (leaves 64-71).
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We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci-e.g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/ approximately pritch/home. html.
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We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations ("admixture linkage disequilibium"). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori, and drift in populations of Drosophila melanogaster. The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu.
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Enge, K.M., M.M. Bentzien, and H.F. Percival. 1986. Florida scrub lizard status survey. a Cooperative Fish and Wildlife Research Unit. Technical Report No. 26. University of a, Gainesville, FL.
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Hill, K. 1999. Responses of released populations of the Florida Sand Skink, Neoseps reynoldsi, to scrub habitat translocation in Central a. Master"s Thesis. University of South Florida, Tampa.
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Knight, G.R., A. Kinght, D. Hipes, K. NeSmith, K. Gulledge, A. Jenkins, C. Elam, P. Diamond, J. Oetting, and A. Newberry. 2010. Development of a cooperative land cover map: final report. Florida " s Wildlife Legacy Initiative Project 08009.
Genetic Data Analysis: computer program for the analysis of allelic data. Version 1.0 (d16c) Software available over the internet from http
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Lewis P. O., and Zaykin, D. 2001 Genetic Data Analysis: computer program for the analysis of allelic data. Version 1.0 (d16c). Software available over the internet from http://hydrodictyon.eeb.uconn.edu/people/plewis/software.php. Cited 10 Dec 2008
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