With the develpment of sequencing technology and experimental protocol, more and more ecological and conservtion researchers have used genomics tools decoding the problem of the ecology and conservation. With the ecological and genomics informations of the threatened species, it maybe very useful for converation or understand the diversity of these speices .The following is a lot of reserach in the Ecological and Conservation Genomics. In here, I just list some reseach paper in the order of the species. 1、Panda Zhao, S., P. Zheng, et al. (2013). Whole genome sequencing of giant pandas provides insights into demographic history and local adaptation. Nat Genet 45(1): 67-71. 2、Polar Bear Hailer, F., V. E. Kutschera, et al. (2012). Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage. Science 336(6079): 344-347. Miller, W., S. C. Schuster, et al. (2012). Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proc Natl Acad Sci U S A 109(36): E2382-2390. Cahill JA, Green RE, Fulton TL, Stiller M, Jay F, et al. (2013) Genomic Evidence for Island Population Conversion Resolves Conflicting Theories of Polar Bear Evolution. PLoS Genet 9(3): e1003345. doi:10.1371/journal.pgen.1003345 3、Tiger Xu et al., The Genetic Basis of White Tigers, Current Biology (2013), j.cub.2013.04.054http://dx.doi.org/10.1016/ 4、T hreespine stickleback Jones, F. C., M. G. Grabherr, et al. (2012). The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484(7392): 55-61. Hohenlohe, P. A., S. Bassham, et al. (2010). Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genet 6(2): e1000862. Catchen, J., S. Bassham, et al. (2013). The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing. Mol Ecol 22(11): 2864-2883. Roesti, M., D. Moser, et al. (2013). Recombination in the threespine stickleback genome patterns and consequences. Mol Ecol 22(11): 3014-3027. 5、 Sturgeon Ogden, R., K. Gharbi, et al. (2013). Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing. Mol Ecol 22(11): 3112-3123. 6、Pacific lamprey Hess, J. E., N. R. Campbell, et al. (2013). Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species. Mol Ecol 22(11): 2898-2916. 7、herring Clupea harengus Corander, J., K. K. Majander, et al. (2013). High degree of cryptic population differentiation in the Baltic Sea herring Clupea harengus. Mol Ecol 22(11): 2931-2940. 8、Senecio lautus Roda, F., L. Ambrose, et al. (2013). Genomic evidence for the parallel evolution of coastal forms in the Senecio lautus complex. Mol Ecol 22(11): 2941-2952. 9、Bank vole (Myodes glareolus) White, T. A., S. E. Perkins, et al. (2013). Adaptive evolution during an ongoing range expansion: the invasive bank vole (Myodes glareolus) in Ireland. Mol Ecol 22(11): 2971-2985. 10、Xiphophorus fish Jones, J. C., S. Fan, et al. (2013). The evolutionary history of Xiphophorus fish and their sexually selected sword: a genome-wide approach using restriction site-associated DNA sequencing. Mol Ecol 22(11): 2986-3001. 11、 Rainbow and westslope cutthroat trout Hohenlohe, P. A., M. D. Day, et al. (2013). Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing. Mol Ecol 22(11): 3002-3013. 12、Lake Whitefish (Coregonus clupeaformis) Gagnaire, P. A., E. Normandeau, et al. (2013). Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake Whitefish (Coregonus clupeaformis). Mol Ecol 22(11): 3036-3048. Hecht, B. C., N. R. Campbell, et al. (2013). Genomewide association reveals genetic basis for the propensity to migrate in wild populations of rainbow and steelhead trout. Mol Ecol 22(11): 3061-3076. 13、Lake Tanganyika cichlid fish and Lake Victoria cichlid fishes Takahashi, T., T. Sota, et al. (2013). Genetic basis of male colour dimorphism in a Lake Tanganyika cichlid fish. Mol Ecol 22(11): 3049-3060. Keller, I., C. E. Wagner, et al. (2013). Population genomic signatures of divergent adaptation, gene flow and hybrid speciation in the rapid radiation of Lake Victoria cichlid fishes. Mol Ecol 22(11): 2848-2863. 14、 Cepaea nemoralis Richards, P. M., M. M. Liu, et al. (2013). RADSeq derived markers flank the shell colour and banding loci of the Cepaea nemoralis supergene. Mol Ecol 22(11): 3077-3089. 15、Dwarf birch (Betula nana) Wang, N., M. Thomson, et al. (2013). Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers. Mol Ecol 22(11): 3098-3111. 16、 Eurasian beaver Senn, H., R. Ogden, et al. (2013). Reference-free SNP discovery for the Eurasian beaver from restriction site-associated DNA paired-end data. Mol Ecol 22(11): 3141-3150. 17、Red abalone (Haliotis rufescens) De Wit P, Palumbi SR (2013) Transcriptomewide polymorphisms of red abalone (Haliotis rufescens) reveal patterns of gene flow and local adaptation. Molecular Ecology, 22, 2884–2897.
Genotyping based on NGS NGS(next generation sequencing) is very useful for genotyping. In recently or in the future, genotyping based on NGS will become very popular. Even in some ways, these technology will replace the SNP array. There are several methods of genotyping based on NGS in the following. • RRL - Reduced Representation Library • GBS - Genotyping By Sequencing • CRoPS - Complexity Reduction of Polymorphic Sequences • MSG - Multiplex Shotgun Genotyping • RAD - Restriction site Associated DNA There are some articles about the above technology: van Tassell, C. P. et al. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nature Methods 5, 247–252 (2008). The first description of the RRL approach using NGS. Andolfatto, P. et al. Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Res.21, 610–617 (2011). The original description of MSG, describing the hidden Markov model approach to imputation of genotypes. van Orsouw, N. J. et al. Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes. PLoS ONE 2, e1172 (2007). The original description of the CRoPS method. Baird, N. A. et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3, e3376 (2008). The original description of high-throughputRAD-seq. Elshire, R. J. et al. A robust, simple genotyping‑by‑sequencing (GBS) approach for high diversity species. PLoS ONE 6, e19379 (2011). The original description of the GBS method.
标签: GBS
