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Genetic Diversity of the Endemic Xantus’ Hummingbird Using 16 Novel Polymorphic Microsatellite Loci, and Their Cross Amplification between Six Related Species

DOI: 10.4236/ojgen.2016.61003, PP. 19-27

Keywords: Baja California Peninsula, Hylocharis xantusii, Microsatellites, Pyrosequencing, Cross-Species Amplification

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A set of 16 microsatellite loci was developed and characterized for the Xantus’ hummingbird (Hylocharis xantusii) by using 454 next-generation sequencing. Twenty-five H. xantusii samples from one population were genotyped; all loci were polymorphic, with the number of alleles ranging from three to ten. The mean observed heterozygosity was 0.681 for all loci. No significant linkage disequilibrium was detected, but five loci (Hxan05, 06, 09, 13 and 14) showed deviation from Hardy-Weinberg equilibrium. These microsatellite loci are the first to be characterized for H. xantusii. A moderate to high level of cross-species amplification was observed across the six hummingbird species (31% - 87.5%), with the best cross amplification results observed in the closest related species (H. leucotis, Cynanthus latirostris, Calypte costae). The availability of these molecular tools allows assessing questions integrating population genetics, ecology, conservation, and evolutionary history for H. xantusii and for other phyogenetically related species.


[1]  Frankham, R., Ballou, J.D. and Briscore, D.A. (2002) Introduction to Conservation Genetics. Cambridge University Press, Cambridge.
[2]  Ando, H., Kaneko, S., Suzuki, H., Horikoshi, K., Takano, H., Ogawa, H. and Isagi, Y. (2011) Genetic Diversity of the Japanese Wood Pigeon, Columba janthina, Endemic to Islands of East Asia, Estimated by Newly Developed Microsatellite Markers. Zoological Science, 28, 891-896.
[3]  Abdelkrim, J., Robertson, B., Stanton, J.A. and Gemmell, N. (2009) Fast, Cost-Effective Development of Species-Specific Microsatellite Markers by Genomic Sequencing. BioTechniques, 46, 185-192.
[4]  Howell, C.A. and Howell, S.N. (2000) Xantus’s Hummingbird (Hylocharis xantusii). The Birds of North America Online, 14.
[5]  González Rubio, C., García-De-León, F.J. and Rodríguez Estrella, R. (2016) Phylogeography of Endemic Xantus’ Hummingbird (Hylocharis xantusii) Show a Different History of Vicariance in the Baja California Peninsula. Unpublished.
[6]  Rodríguez-Estrella, R., Rubio, L. and Pineda, E. (1997) Los oasis como parches atractivos para lasavesterrestres residentes e invernantes. In: Arriaga, L. and Rodríguez-Estrella, R., Eds., Los Oasis de la Península de Baja California, Mexico, Centro de InvestigacionesBiológicas del Noroeste, La Paz, BCS, Mexico, 157-196.
[7]  Rodríguez-Estrella, R., Blázquez, M.C. and Lobato, J.M. (2005) Avian Communities of Arroyos and Desert Oases in Baja California Sur: Implications for Conservation. In: Cartron, J.L.E., Ceballos, G. and Felger, R.S., Eds., Biodiversity and Conservation in Northern Mexico, Oxford University Press, UK, 334-353.
[8]  Riddle, B.R., Hafner, D.J., Alexander, L.F. and Jaeger, J.R. (2000) Cryptic Vicariance in the Historical Assembly of a Baja California Peninsular Desert Biota. Proceedings National Academy of Sciences, 97, 14438-14443.
[9]  Hernández Baños, B.E., Zamudio Beltrán, L.E., Eguiarte Fruns, L.E., Klicka, J. and García Moreno, J. (2014) The Basilinna Genus (Aves: Trochilidae): An Evaluation Based on Molecular Evidence and Implications for the Genus Hylocharis. Revista Mexicana de Biodiversidad, 85, 797-807.
[10]  Aljanabi, S.M. and Martínez, I. (1997) Universal and Rapid Salt-Extraction of High Quality Genomic DNA for PCR-Based Techniques. Nucleic Acids Research, 25, 4692-4693.
[11]  Lozano Garza, O.A., León de la Luz, J.L., Lara, S.F. and García-De-León, F.J. (2015) New Interpretations about Clonal Architecture for the Sour Pitaya (Stenocereus gummosus, Cactaceae), Arising from Microsatellite Markers of de Novo Isolation and Characterization. Open Journal of Genetics, 5, 1-11.
[12]  Faircloth, B.C. (2008) Msatcommander: Detection of Microsatellite Repeat Arrays and Automated, Locus-Specific Primer Design. Molecular Ecology Resources, 8, 92-94.
[13]  Meglécz, E., Costedoat, C., Dubut, V., Gilles, A., Malausa, T., Pech, N. and Martin, J.-F. (2010) QDD: A User-Friendly Program to Select Microsatellite Markers and Design Primers from Large Sequencing Projects. Bioinformatics, 26, 403-404.
[14]  Chapuis, M.P. and Estoup, A. (2007) Microsatellite Null Alleles and Estimation of Population Differentiation. Molecular Biology and Evolution, 24, 621-631.
[15]  Peakall, R. and Smouse, P.E. (2012) GenAlEx 6.5: Genetic Analysis in Excel. Population Genetic Software for Teaching and Research—An Update. Bioinformatics, 28, 2537-2539.
[16]  Rousset, F. (2008) GENEPOP’007: A Complete Re-Implementation of the Genepop Software for Windows and Linux. Molecular Ecology Resources, 8, 103-106.
[17]  González, C., Ornelas, J.F. and Gutiérrez Rodríguez, C. (2011) Selection and Geographic Isolation Influence Hummingbird Speciation: Genetic, Acoustic and Morphological Divergence in the Wedge-Tailed Sabrewing (Campylopterus curvipennis). BMC Evolutionary Biology, 11, 38.
[18]  González, C. and Ornelas, J.F. (2014) Acoustic Divergence with Gene Flow in a Lekking Hummingbird with Complex Songs. PLoS ONE, 9, e109241.
[19]  Mukesh Javed, R., Gaur, U., Jianlin, H. and Sathyakumar, S. (2011) Cross-Species Applicability of Chicken Microsatellite Markers for Investigation of Genetic Diversity in Indian Duck (Anasplatyrhynchos) Populations. African Journal of Biotechnology, 10, 17623-17631.
[20]  Qu, Y., Luo, X., Zhang, R., Song, G., Zou, F. and Lei, F. (2011) Lineage Diversification and Historical Demography of a Montane Bird Garrulaxelliotii—Implications for the Pleistocene Evolutionary History of the Eastern Himalayas. BMC Evolutionary Biology, 11, 174.
[21]  Rollins, L.A., Browning, L.E., Holleley, C.E., Sabage, J.L., Russell, A.F. and Griffith, S.C. (2012) Building Genetic Networks Using Relatedness Information: A Novel Approach for the Estimation of Dispersal and Characterization of Group Structure in Social Animals. Molecular Ecology, 21, 1727-1740.
[22]  Jiang, H.X., Ren, S.L., Hou, Y.Q., Yang, M. and Wu, X.B. (2011) Isolation and Characterization of Tetranucleotide Repeat Polymorphic Microsatellite Loci in Larussaundersi (Aves, Laridae). Genetic Molecular Resources, 10, 2034-2037.
[23]  Parada, R., Ksiazkiewicz, J., Kawka, M. and Jaszczak, K. (2012) Studies on Resources of Genetic Diversity in Conservative Flocks of Geese Using Microsatellite DNA Polymorphic Markers. Molecular Biology Reports, 39, 5291-5297.
[24]  Eltanany, M., Philipp, U., Weigend, S. and Distl, O. (2011) Genetic Diversity of Ten Egyptian Chicken Strains Using 29 Microsatellite Markers. Animal Genetics, 42, 666-669.
[25]  Mukesh and Sathyakumar, S. (2011) Eighteen Polymorphic Microsatellites for Domestic Pigeon Columba livia var. domestica Developed by Cross Species Amplification of Chicken Markers. Journal of Genetics, 90, 86-89.
[26]  Santos, D.O., Moreira, L.R., Tonhati, H. and Caparroz, R. (2012) Isolation and Characterization of Ten Novel Microsatellite Loci in the Red-Winged Tinamou (Rhynchotusrufescens, Tinamiformes, Aves) and Cross-Amplification in Other Tinamous. Molecular Biology Reports, 39, 4837-4840.
[27]  Wang, H., Lou, X., Zhu, Q., Huang, Y., Zhou, L. and Zhang, B. (2011) Isolation and Characterization of Microsatellite DNA Markers for the Oriental White Stork, Ciconiaboyciana. Zoological Science, 28, 606-608.


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