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Rc\Jd S£P 23 2015 ARIZONA STATE UNIVERSITY Molecular Anthropology Laboratory Division of Management Authority US Fish and Wildlife Service RC\JD S£P 23 2015 4401 North Fairfax Dr., Room 700 Arlington, VA 22203 fax: (703) 358-2281 September 9, 2015 Dear Sir or Madam, Enclosed please find an updated renewal application for CITES pennit {#14US094332/9). I am not requesting any changes to the original application. This year, the Molecular Anthropology Laboratory did not import any samples under this CITES permit. We hope to import additional DNA samples during the next year from Africa. These DNA samples are being used for long term scientific research on population genetics and the evolutionary history of great apes and to study the impact of mycobacteria such as M. tuberculosis on primate health and conservation. Better understanding of the population genetics and evolutionary history of the great apes as well as how different bacteria affect their health (and whether they are exchanging disease organisms with humans} will facilitate ongoing conservation efforts of these species. Please contact me with any additional questions. Thank you for your assistance. Sincerely, Anne C. Stone, Ph.D. Laboratory Director Professor [email protected] COLLEGE OF LIBERAL ARTS AND SciENCES School of Human Evolution & Social Change PO Box 872402, Tempe, AZ 85287-2402 {480) 965-6213 FAX: (480) 965-7671 Responses to questions on page 2 on the Pennit application fonn (renewal) 1: pennit number 14US094332/9. 2: The original pennit is attached as Appendix A. 3: This past year, the ASU Molecular Anthropology Laboratory did not import specimens under this CITES permit. The Molecular Anthropology Laboratory is seeking a reissuance/renewal of the pennit because we hope to import additional samples from great apes in the coming year for the projects described below in the annual report. 4. Annual Report: This permit {#14US094332/9) did not include the usual stipulations for an annual report. Here, I provide an annual report as per the stipulations in the previous version (#09US09433219). No samples were imported this year. The laboratory's research focuses on understanding population genetic variation and evolutionary history of Hominoids (humans and great apes) and we focus on the distribution and evolutionary history of primate diseases such as mycobacteria. Thus, this research requires large sample sizes to address our questions. In particular, we are examining genetic diversity using mitochondrial, Y chromosome, and autosomal loci in order to understand the population structure and history of great apes. Currently, I am collaborating with Dr. Yoav Gilad (University of Chicago), Dr. Reed Cartwright, Dr. Melissa Wilson-Sayres, and Dr. Ian Gilby (Arizona State University), to examine great ape genetic variation. The major aims of this project are ( 1) to characterize diversity patterns and infer the demographic history of a large set of primates, providing the first large scale comparison of evolutionary history of primates, (2) to infer fine-scale recombination rate and characterize the decay of linkage disequilibrium in apes, and (3) to learn about speciation events in primates, particularly in apes, as well as address questions about ancient human population structure and possible early human-chimpanzee admixture. These questions are best addressed by combining polymorphism and divergence data, and analyzing multiple populations of each species, (4) to estimate selection coefficients acting on mutations within and between primates, allowing us to address long-standing questions about the efficacy of natural selection in different populations. In particular, we will be able to examine how differences in mutation rate, recombination rate and effective population size affect the efficacy of selection, and (5) to evaluate the effect of generation time on mutation rates. with important implications for our understanding of the mutation process in primates. All of this basic scientific research aids in our understanding ofspecies structure and will then facilitate conservation of remaining wild species and better preservation and maintenance of captive populations. At present, I am also completing a population structural analysis of mitochondrial sequences (both short fragments and the complete mitochondrial genome) in over 200 chimpanzees (representing all recognized and proposed subspecies). Over the last 15 years, I have also used these data as well as those from the Y chromosome analyses to aid zoos, primate centers and sanctuaries in subspecies identification. This enables them to better manage the captive popu1ation and, in the case of sanctuaries, provide an indication of where individua1s are likely to have been poached. It has also resulted in better infonnation on educational displays at zoos. Finally, in collaboration with Dr. Katherine Detweiler (Florida Atlantic U.), Dr. Andrew Hill and Dr. Brenda Bradley (Yale}, Dr. John Mitani (University of Michigan), Dr. Michelle Sauther (Colorado) and Drs. Alicia Wilbur and Lisa Jones-Engel (University of Washington National Primate Research Center), I am also investigating disease in primates. In particular, we are interested in the distribution ofleprosy and tuberculosis in wild animals, as well as in better understanding the different strains of these pathogens that affect primates. To date, we have sequenced the genome of a strain of leprosy isolated from a mangabey, and we are currently analyzing a strain that was isolated from a chimpanzee. The results of all of this research will be published in scientific journals, presented at scientific meetings and provided to non-governmental organizations such as the Jane Goodall Institute, Lukuru Fowtdation, the Pan African Sanctuary Alliance (PASA), the Bonobo and Congo Biodiversity Initiative (sponsored by the Zoological Society ofMilwaukee), the World Wildlife Fund and other conservation groups. Previous publications :from our research include: Ferreira Z, Hurle B, Andres A, Kretzschmar W, Mullikin J, Cheruk.uri P, Cruz P, Gonder MK, Stone AC, TishkoffS, Swanson W, NISC Comparative Sequencing Program, Clark AG, Green E, and Seixas S. (2013) Sequence diversity of Pan troglodytes subspecies and the impact of WFDC6 selective constraints in reproductive immwtity. Genome Biology and Evolution 5:2512- 2523 Iskow RC, Gokcumen 0, Abyzov A, Malukiewicz J, Zhu Q, Sukumar AT, Pai AA, Mills RE, Habegger L, Cusanovich DA, Rubel MA, Perry GH, Gerstein M, Stone AC, Gi1ad Y, and Lee C. (2012) Regulatory element copy number differences shape primate expression profiles. Proceedings of the National Academy of Sciences, USA 109:12656-12661. Ferguson W, Dvora S, Stone AC, and Boissinot S. (2012) Long-tenn balancing selection at the antiviral gene OAS 1 in central African chimpanzees. Molecular Biology and Evolution. 29:1093-103 Stone AC, Battistuzzi F, Kubatko LS, Perry GH, Trudeau E, Lin H, and Kumar S. (2010) Analysis of complete mtDNA sequences in Pan. Proceedings of the Royal Society, Series B. 365:3277-3288. Claw KG, Tito RY, Stone AC, and Verrelli BC. (2010) Haplotype structure and divergence at human and chimpanzee serotonin transporter and receptor genes: implications for behavioral disorder association analyses. Molecular Biology and Evolution 27:1518-29 VerreJii BC, Stone AC, and Lewis CM. (2008) Different Selective Pressures Shape the Molecular Evolution of Color Vision in Human and Chimpanzee Populations. Molecular Biology and Evolution 25: 2735-43 Perry GH, Yang F, Marques-Bonet T, Murphy C, Fitzgerald T, Lee AS, Hyland C, Smith RS, Stone AC, Hurles ME, Tyler-Smith C, Eichler EE, Carter NP, Lee C, and Redon R. (2008) Copy number variation and genome evolution in humans and chimpanzees. Genome Research 18:1698-1710. Becquet C, Patterson N, Stone A, Przeworski M, and Reich D. (2007) Elucidating the population structure of chimpanzees. PLOS Genetics. Apr 20;3(4):e66. Verrelli BC, Tishkofl'SA, Stone AC and Touclunan JW. (2006} Contrasting histories of G6PD molecular evolution and malarial resistance in humans and chimpanzees. Molecular Biology and Evolution. 23:1592-1601. Stone et al. 2002, High levels ofY-chromosome nucleotide diversity in the genus Pan troglodytes. Proceedings ofthe National Academy of Sciences. USA 99:43-48 These projects have been funded by the National Science Foundation and the National Institutes of Health. To date, these projects support the division of chimpanzees into three subspecies but indicate that there may be some substructure within western chimpanzee (Pan troglodytes verus). The taxonomic status of the proposed fourth subspecies (Pan troglodytes e/lioti fonnerly known asP. 1. vellerosus) is still unclear from these studies and warrants further research. OMB No. 1018-0093 Department of the Interior E:opira OS/31/2011 U.S. Fish and Wildlife Service Federal Fish and Wildlife Permit Application FoiWUDSEP 23 2.015 Rtturn to: U.S. Fish and Wildlife Service Type of Activity: (Enter address from pages 4 and S ofapplicat ion) REISSUANCE, RENEWAL, OR AMENDMENT OF A PERMIT (For this application, all permits, registrations, and certificates aro referred to as a permit.) Complete Sections A orB, C, 0, and E ofthis application. U.S. address may be required in Section C, see instructions for details. Sec attached irutruclicm pages for information on how to make yoar applieation complete and help avoid unnecessary delays. A. Complete if applyine; as an individual I a. Last name l.b fir.stname I.e. Middle name or initial I.<L Suffix 2 Date ofb1rth (mmlddlyyyy}
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