[1] |
Ai, H., Fang, X., Yang, B. et al. Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing Nat. Genet., 47 (2015),pp. 217-225
|
[2] |
Allendorf, F.W., Hohenlohe, P.A., Luikart, G. Genomics and the future of conservation genetics Nat. Rev. Genet., 11 (2010),pp. 697-709
|
[3] |
Amaral, A.R., Beheregaray, L.B., Bilgmann, K. et al. PLoS One, 7 (2012)
|
[4] |
Avise, J. Perspective: conservation genetics enters the genomics era. 2009 Conserv. Genet., 11 (2010),pp. 665-669
|
[5] |
Behjati, S., Tarpey, P.S. What is next generation sequencing? Arch. Dis. Child. Educ. Pract. Ed., 98 (2013),pp. 236-238
|
[6] |
Berg, P.R., Jentoft, S., Star, B. et al. Genome Biol. Evol., 7 (2015),pp. 1644-1663
|
[7] |
Bonnel, M.L., Selander, R.K. Elephant seals: genetic variation and near extinction Science, 184 (1974),pp. 908-909
|
[8] |
Borthakur, U., Barman, R.D., Das, C. et al. Eur. J. Wildl. Res., 57 (2011),pp. 603-613
|
[9] |
Burton, J.N., Adey, A., Patwardhan, R.P. et al. Nat. Biotechnol., 31 (2013),pp. 1119-1125
|
[10] |
Cai, Q., Qian, X., Lang, Y. et al. Genome Biol., 14 (2013),p. R29
|
[11] |
Cho, Y.S., Hu, L., Hou, H. et al. The tiger genome and comparative analysis with lion and snow leopard genomes Nat. Commun., 4 (2013),p. 2433
|
[12] |
Christin, P.A., Weinreich, D.M., Besnard, G. Causes and evolutionary significance of genetic convergence Trends Genet., 26 (2010),pp. 400-405
|
[13] |
David, H.R., Richard, F. Correlation between fitness and genetic diversity Conserv. Biol., 17 (2003),pp. 230-237
|
[14] |
Frankel, O., Soulé, M.E.
|
[15] |
Frankham, R. Genetics and extinction Biol. Conserv., 126 (2005),pp. 131-140
|
[16] |
Frankham, R. Challenges and opportunities of genetic approaches to biological conservation Biol. Conserv., 143 (2010),pp. 1919-1927
|
[17] |
Frankham, R., Ballou, J.D., Briscoe, D.A.
|
[18] |
Ge, R.L., Cai, Q., Shen, Y.Y. et al. Draft genome sequence of the Tibetan antelope Nat. Commun., 4 (2013),p. 1858
|
[19] |
Gutenkunst, R.N., Hernandez, R.D., Williamson, S.H. et al. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data PLoS Genet., 5 (2009)
|
[20] |
Hagen, S.B., Kopatz, A., Aspi, J. et al. Evidence of rapid change in genetic structure and diversity during range expansion in a recovering large terrestrial carnivore Proc. R. Soc. B, 282 (2015)
|
[21] |
Hausknecht, R., Bayerl, H., Gula, R. et al. Application of quantitative real-time polymerase chain reaction for noninvasive genetic monitoring J. Wildl. Manag., 74 (2010),pp. 1904-1910
|
[22] |
Hoffmann, A.A., Sgrò, C.M. Climate change and evolutionary adaptation Nature, 470 (2011),p. 479
|
[23] |
Holderegger, R., Wagner, H.H. Landscape genetics Bioscience, 58 (2008),pp. 199-207
|
[24] |
Hu, J.C.
|
[25] |
Hu, Y., Qi, D., Wang, H. et al. Genetic evidence of recent population contraction in the southernmost population of giant pandas Genetica, 138 (2010),pp. 1297-1306
|
[26] |
Hu, Y., Zhan, X., Qi, D. et al. Spatial genetic structure and dispersal of giant pandas on a mountain-range scale Conserv. Genet., 11 (2010),pp. 2145-2155
|
[27] |
Hu, Y., Nie, Y., Wei, W. et al. Inbreeding and inbreeding avoidance in wild giant pandas Mol. Ecol., 26 (2017),pp. 5793-5806
|
[28] |
Hu, Y., Wu, Q., Ma, S. et al. Comparative genomics reveals convergent evolution between the bamboo-eating giant and red pandas Proc. Natl. Acad. Sci. U. S. A., 114 (2017),pp. 1081-1086
|
[29] |
Jiao, Y., Peluso, P., Shi, J. et al. Improved maize reference genome with single-molecule technologies Nature, 546 (2017),pp. 524-527
|
[30] |
Joost, S., Bonin, A., Bruford, M.W. et al. A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation Mol. Ecol., 16 (2007),pp. 3955-3969
|
[31] |
Kim, J., Farré, M., Auvil, L. et al. Reconstruction and evolutionary history of eutherian chromosomes Proc. Natl. Acad. Sci. U. S. A., 114 (2017),pp. e5379-e5388
|
[32] |
Kohn, M.H., Murphy, W.J., Ostrander, E.A. et al. Genomics and conservation genetics Trends Ecol. Evol., 21 (2006),pp. 629-637
|
[33] |
Kronenberg, Z.N., Fiddes, I.T., Gordon, D. et al. High-resolution comparative analysis of great ape genomes Science, 360 (2018)
|
[34] |
Leamy, L.J., Lee, C.R., Song, Q. et al. Ecol. Evol., 6 (2016),pp. 6332-6344
|
[35] |
Lee, H., Gurtowski, J., Yoo, S. et al. Third-generation sequencing and the future of genomics BioRxiv (2016)
|
[36] |
Li, H., Durbin, R. Inference of human population history from individual whole-genome sequences Nature, 475 (2011),p. 493
|
[37] |
Li, R., Fan, W., Tian, G. et al. Nature, 463 (2010),pp. 311-317
|
[38] |
Li, M., Tian, S., Jin, L. et al. Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars Nat. Genet., 45 (2013),pp. 1431-1438
|
[39] |
Ling, H.Q., Ma, B., Shi, X. et al. Nature, 557 (2018),pp. 424-428
|
[40] |
Liu, Z., Wang, B., Nadler, T. et al. Relatively recent evolution of pelage coloration in Colobinae: phylogeny and phylogeography of three closely related langur species PloS One, 8 (2013)
|
[41] |
Liu, S., Lorenzen, E.D., Fumagalli, M. et al. Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears Cell, 157 (2014),pp. 785-794
|
[42] |
Lu, Z., Johnson, W.E., Menotti-Raymond, M. et al. Patterns of genetic diversity in remaining giant panda populations Conserv. Biol., 15 (2001),pp. 1596-1607
|
[43] |
Luikart, G., England, P.R., Tallmon, D. et al. The power and promise of population genomics: from genotyping to genome typing Nat. Rev. Genet., 4 (2003),pp. 981-994
|
[44] |
Ma, T., Hu, Y., Russo, I. et al. Walking in a heterogeneous landscape: dispersal, gene-flow and conservation implications for the giant panda in the Qinling Mountains Evol. Appl. (2018)
|
[45] |
Manel, S., Holderegger, R. Ten years of landscape genetics Trends Ecol. Evol., 28 (2013),pp. 614-621
|
[46] |
Manel, S., Schwartz, M.K., Luikart, G. et al. Landscape genetics: combining landscape ecology and population genetics Trends Ecol. Evol., 18 (2003),pp. 189-197
|
[47] |
Manel, S., Joost, S., Epperson, B.K. et al. Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field Mol. Ecol., 19 (2010),pp. 3760-3772
|
[48] |
Manthey, J.D., Moyle, R.G. Mol. Ecol., 24 (2015),pp. 3628-3638
|
[49] |
Mendez, M., Subramaniam, A., Collins, T. et al. Molecular ecology meets remote sensing: environmental drivers to population structure of humpback dolphins in the Western Indian Ocean Heredity, 107 (2011),p. 349
|
[50] |
Meyerhof, W., Batram, C., Kuhn, C. et al. Chem. Senses, 35 (2010),pp. 157-170
|
[51] |
Moritz, C. Strategies to protect biological diversity and the evolutionary processes that sustain it Syst. Biol., 51 (2002),pp. 238-254
|
[52] |
Mullis, K.B., Faloona, F.A. Methods Enzymol., 155 (1987),pp. 335-350
|
[53] |
O'brien, S.J., Wildt, D.E., Goldman, D. et al. The cheetah is depauperate in genetic variation Science, 221 (1983),pp. 459-462
|
[54] |
Ouborg, N.J., Pertoldi, C., Loeschcke, V. et al. Conservation genetics in transition to conservation genomics Trends Genet., 26 (2010),pp. 177-187
|
[55] |
Pendleton, M., Sebra, R., Pang, A.W. et al. Assembly and diploid architecture of an individual human genome via single-molecule technologies Nat. Methods, 12 (2015),pp. 780-786
|
[56] |
Picelli, S., Faridani, O.R., Bjorklund, A.K. et al. Full-length RNA-seq from single cells using Smart-seq2 Nat. Protoc., 9 (2014),pp. 171-181
|
[57] |
Pompanon, F., Bonin, A., Bellemain, E. et al. Genotyping errors: causes, consequences and solutions Nat. Rev. Genet., 6 (2005),p. 847
|
[58] |
Qiu, Q., Zhang, G., Ma, T. et al. The yak genome and adaptation to life at high altitude Nat. Genet., 44 (2012),pp. 946-949
|
[59] |
Qiu, Q., Wang, L., Wang, K. et al. Yak whole-genome resequencing reveals domestication signatures and prehistoric population expansions Nat. Commun., 6 (2015),p. 10283
|
[60] |
Qu, Y., Zhao, H., Han, N. et al. Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau Nat. Commun., 4 (2013),p. 2071
|
[61] |
Ralls, K., Brugger, K., Ballou, J. Inbreeding and juvenile mortality in small populations of ungulates Science, 206 (1979),pp. 1101-1103
|
[62] |
Ryder, O.A. Conservation genomics: applying whole genome studies to species conservation efforts Cytogenet. Genome Res., 108 (2005),pp. 6-15
|
[63] |
Saiki, R.K., Gelfand, D.H., Stoffel, S. et al. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase Science, 239 (1988),pp. 487-491
|
[64] |
Sanger, F., Coulson, A.R. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase J. Mol. Biol., 94 (1975),pp. 441-448
|
[65] |
Schaller, G.B., Hu, J.C., Pan, W.S. et al.
|
[66] |
Schatz, M.C., Delcher, A.L., Salzberg, S.L. Assembly of large genomes using second-generation sequencing Genome Res., 20 (2010),pp. 1165-1173
|
[67] |
Schiffels, S., Durbin, R. Inferring human population size and separation history from multiple genome sequences Nat. Genet., 46 (2014),pp. 919-925
|
[68] |
Schlotterer, C. Hitchhiking mapping--functional genomics from the population genetics perspective Trends Genet., 19 (2003),pp. 32-38
|
[69] |
Schonewald-Cox, C., Chambers, S., MacBryde, B. et al.
|
[70] |
Shafer, A.B., Wolf, J.B., Alves, P.C. et al. Genomics and the challenging translation into conservation practice Trends Ecol. Evol., 30 (2015),pp. 78-87
|
[71] |
Shan, L., Hu, Y., Wei, F. Opportunities and challenges of fecal DNA technology in molecular ecology researches Acta Theriol. Sin., 38 (2018),pp. 235-246
|
[72] |
Shan, L., Wu, Q., Wang, L. et al. Lineage-specific evolution of bitter taste receptor genes in the giant and red pandas implies dietary adaptation Integr. Zool., 13 (2018),pp. 152-159
|
[73] |
Sharon, D., Tilgner, H., Grubert, F. et al. A single-molecule long-read survey of the human transcriptome Nat. Biotechnol., 31 (2013),pp. 1009-1014
|
[74] |
Steiner, C.C., Putnam, A.S., Hoeck, P.E. et al. Conservation genomics of threatened animal species Annu. Rev. Anim. Biosci., 1 (2013),pp. 261-281
|
[75] |
Stern, D.L. The genetic causes of convergent evolution Nat. Rev. Genet., 14 (2013),p. 751
|
[76] |
Storz, J.F. Causes of molecular convergence and parallelism in protein evolution Nat. Rev. Genet., 17 (2016),pp. 239-250
|
[77] |
Sun, Y.B., Xiong, Z.J., Xiang, X.Y. et al. Proc. Natl. Acad. Sci. U. S. A., 112 (2015),pp. 1257-1262
|
[78] |
Taberlet, P., Griffin, S., Goossens, B. et al. Reliable genotyping of samples with very low DNA quantities using PCR Nucleic Acids Res., 24 (1996),pp. 3189-3194
|
[79] |
Taberlet, P., Waits, L.P., Luikart, G. Noninvasive genetic sampling: look before you leap Nat. Rev. Genet., 14 (1999),pp. 323-327
|
[80] |
Wan, Q.H., Pan, S.K., Hu, L. et al. Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator Cell Res., 23 (2013),pp. 1091-1105
|
[81] |
Wang, J., Wang, W., Li, R. et al. The diploid genome sequence of an Asian individual Nature, 456 (2008),pp. 60-65
|
[82] |
Wang, D., Hu, Y., Ma, T. et al. Noninvasive genetics provides insights into the population size and genetic diversity of an Amur tiger population in China Integr. Zool., 11 (2016),pp. 16-24
|
[83] |
Wei, F., Hu, Y., Zhu, L. et al. Black and white and read all over: the past, present and future of giant panda genetics Mol. Ecol., 21 (2012),pp. 5660-5674
|
[84] |
Wei, F., Hu, Y., Yan, L. et al. Giant pandas are not an evolutionary cul-de-sac: evidence from multidisciplinary research Mol. Biol. Evol., 32 (2015),pp. 4-12
|
[85] |
Wu, Q., Wang, Y., Ding, Y. et al. A natural communication system on genome evolution Sci. China Life Sci., 60 (2017),pp. 432-435
|
[86] |
Yan, F., Lu, J., Zhang, B. et al. The Chinese giant salamander exemplifies the hidden extinction of cryptic species Curr. Biol., 28 (2018),pp. R590-R592
|
[87] |
Yang, J., Jiang, Z. Conserv. Genet., 12 (2011),pp. 1457-1468
|
[88] |
Yang, J., Jiang, Z., Zeng, Y. et al. Effect of anthropogenic landscape features on population genetic differentiation of Przewalski's gazelle: main role of human settlement PloS One, 6 (2011)
|
[89] |
Yin, W., Wang, Z.J., Li, Q.Y. et al. Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper Nat. Commun., 7 (2016),p. 13107
|
[90] |
Yu, L., Wang, G.D., Ruan, J. et al. Nat. Genet., 48 (2016),p. 947
|
[91] |
Zhan, X., Li, M., Zhang, Z. et al. Molecular censusing doubles giant panda population estimate in a key nature reserve Curr. Biol., 16 (2006),pp. R451-R452
|
[92] |
Zhan, X.J., Zhang, Z.J., Wu, H. et al. Molecular analysis of dispersal in giant pandas Mol. Ecol., 16 (2007),pp. 3792-3800
|
[93] |
Zhan, X., Zheng, X., Bruford, M.W. et al. A new method for quantifying genotyping errors for noninvasive genetic studies Conserv. Genet., 11 (2010),pp. 1567-1571
|
[94] |
Zhan, X., Pan, S., Wang, J. et al. Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle Nat. Genet., 45 (2013),pp. 563-566
|
[95] |
Zhang, J., Zhang, Y.P., Rosenberg, H.F. Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey Nat. Genet., 30 (2002),pp. 411-415
|
[96] |
Zhang, B., Li, M., Zhang, Z. et al. Genetic viability and population history of the giant panda, putting an end to the "evolutionary dead end"? Mol. Biol. Evol., 24 (2007),pp. 1801-1810
|
[97] |
Zhang, F., Jiang, Z., Xu, A. et al. Recent geological events and intrinsic behavior influence the population genetic structure of the chiru and Tibetan gazelle on the Tibetan plateau PloS One, 8 (2013)
|
[98] |
Zhang, G., Li, C., Li, Q. et al. Comparative genomics reveals insights into avian genome evolution and adaptation Science, 346 (2014),pp. 1311-1320
|
[99] |
Zhao, T.B., Ning, H.X., Zhu, S.S. et al. Biochem. Biophys. Res. Commun., 316 (2004),pp. 565-572
|
[100] |
Zhao, H., Yang, J.R., Xu, H. et al. Mol. Biol. Evol., 27 (2010),pp. 2669-2673
|
[101] |
Zhao, S., Zheng, P., Dong, S. et al. Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation Nat. Genet., 45 (2013),pp. 67-71
|
[102] |
Zhou, X., Sun, F., Xu, S. et al. Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations Nat. Commun., 4 (2013),p. 2708
|
[103] |
Zhou, X., Wang, B., Pan, Q. et al. Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history Nat. Genet., 46 (2014),pp. 1303-1310
|
[104] |
Zhou, X., Meng, X., Liu, Z. et al. Population genomics reveals low genetic diversity and adaptation to hypoxia in snub-nosed monkeys Mol. Biol. Evol., 33 (2016),pp. 2670-2681
|
[105] |
Zhou, X., Guang, X., Sun, D. et al. Population genomics of finless porpoises reveal an incipient cetacean species adapted to freshwater Nat. Commun., 9 (2018),p. 1276
|
[106] |
Zhu, L., Zhan, X., Wu, H. et al. Conservation implications of drastic reductions in the smallest and most isolated populations of giant pandas Conserv. Biol., 24 (2010),pp. 1299-1306
|
[107] |
Zhu, L., Zhang, S., Gu, X. et al. Significant genetic boundaries and spatial dynamics of giant pandas occupying fragmented habitat across southwest China Mol. Ecol., 20 (2011),pp. 1122-1132
|