The Promise and Practicality of Population Genomics Research with Endangered Species

International Journal of Primatology

Volumn 35, Issue 1, 2014, Pages 55-70

  Perry, George H ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Conservation genomics; Massively parallel sequencing; Nonmodel species; Population genomics

Indexed keywords

EID: 84893785685     PISSN: 01640291     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10764-013-9702-z     Document Type: Article

References (56)

1. Albert, T. J., Molla, M. N., Muzny, D. M., Nazareth, L., Wheeler, D., Song, X., et al. (2007). Direct selection of human genomic loci by microarray hybridization. Nature Methods, 4(11), 903-905.
2. Allendorf, F. W., Hohenlohe, P. A., & Luikart, G. (2010). Genomics and the future of conservation genetics. Nature Reviews Genetics, 11(10), 697-709.
3. Amato, K. R., Yeoman, C. J., Kent, A., Righini, N., Carbonero, F., Estrada, A., et al. (2013). Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. The ISME Journal, 7(7), 1344-1353.
4. Arandjelovic, M., Guschanski, K., Schubert, G., Harris, T. R., Thalmann, O., Siedel, H., et al. (2009). Two-step multiplex polymerase chain reaction improves the speed and accuracy of genotyping using DNA from noninvasive and museum samples. Molecular Ecology Resources, 9, 28-36.
5. Baird, N. A., Etter, P. D., Atwood, T. S., Currey, M. C., Shiver, A. L., Lewis, Z. A., et al. (2008). Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One, 3(10), e3376.
6. Bell, O., Tiwari, V. K., Thoma, N. H., & Schubeler, D. (2011). Determinants and dynamics of genome accessibility. Nature Reviews Genetics, 12(8), 554-564.
7. Bergey, C. M., Pozzi, L., Disotell, T. R., & Burrell, A. S. (2013). A new method for genome-wide marker development and genotyping holds great promise for molecular primatology. International Journal of Primatology, 34(2), 303-314.
8. Bock, C. (2012). Analysing and interpreting DNA methylation data. Nature Reviews Genetics, 13(10), 705-719.
9. Briggs, A. W., Good, J. M., Green, R. E., Krause, J., Maricic, T., Stenzel, U., et al. (2009). Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science, 325, 318-321.
10. Buchan, J. C., Archie, E. A., van Horn, R. C., Moss, C. J., & Alberts, S. C. (2005). Locus effects and sources of error in noninvasive genotyping. Molecular Ecology Notes, 5, 680-683.
11. Burbano, H. A., Hodges, E., Green, R. E., Briggs, A. W., Krause, J., Meyer, M., et al. (2010). Targeted investigation of the Neandertal genome by array-based sequence capture. Science, 328(5979), 723-725.
12. Degnan, P. H., Pusey, A. E., Lonsdorf, E. V., Goodall, J., Wroblewski, E. E., Wilson, M. L., et al. (2012). Factors associated with the diversification of the gut microbial communities within chimpanzees from Gombe National Park. Proceedings of the National Academy of Sciences of the USA, 109(32), 13034-13039.
13. Ekblom, R., Farrell, L. L., Lank, D. B., & Burke, T. (2012). Gene expression divergence and nucleotide differentiation between males of different color morphs and mating strategies in the ruff. Ecology & Evolution, 2(10), 2485-2505.
14. Ekblom, R., & Galindo, J. (2011). Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity, 107(1), 1-15.
15. Fonseca, N. A., Rung, J., Brazma, A., & Marioni, J. C. (2012). Tools for mapping high-throughput sequencing data. Bioinformatics, 28(24), 3169-3177.
16. Gayral, P., Weinert, L., Chiari, Y., Tsagkogeorga, G., Ballenghien, M., & Galtier, N. (2011). Next-generation sequencing of transcriptomes: A guide to RNA isolation in nonmodel animals. Molecular Ecology Resources, 11(4), 650-661.
17. George, R. D., McVicker, G., Diederich, R., Ng, S. B., MacKenzie, A. P., Swanson, W. J., et al. (2011). Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection. Genome Research, 21(10), 1686-1694.
18. Glenn, T. C. (2011). Field guide to next-generation DNA sequencers. Molecular Ecology Resources, 11(5), 759-769.
19. Gnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E. M., Brockman, W., et al. (2009). Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nature Biotechnology, 27, 182-189.
20. Guschanski, K., Krause, J., Sawyer, S., Valente, L. M., Bailey, S., Finstermeier, K., et al. (2013). Next-generation museomics disentangles one of the largest primate radiations. Systematic Biology, 62(4), 539-554.
21. Hohenlohe, P. A., Day, M. D., Amish, S. J., Miller, M. R., Kamps-Hughes, N., Boyer, M. C., et al. (2013). Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing. Molecular Ecology, 22(11), 3002-3013.
22. International Human Genome Sequencing Consortium. (2004). Finishing the euchromatic sequence of the human genome. Nature, 431, 931-945.
23. Jennings, T. N., Knaus, B. J., Mullins, T. D., Haig, S. M., & Cronn, R. C. (2011). Multiplexed microsatellite recovery using massively parallel sequencing. Molecular Ecology Resources, 11(6), 1060-1067.
24. Kohn, M. H. (2010). Noninvasive genome sampling in chimpanzees. Molecular Ecology, 19(24), 5328-5331.
25. Kuczynski, J., Lauber, C. L., Walters, W. A., Parfrey, L. W., Clemente, J. C., Gevers, D., et al. (2012). Experimental and analytical tools for studying the human microbiome. Nature Reviews Genetics, 13(1), 47-58.
26. Leffler, E. M., Bullaughey, K., Matute, D. R., Meyer, W. K., Segurel, L., Venkat, A., et al. (2012). Revisiting an old riddle: What determines genetic diversity levels within species? PLoS Biology, 10(9), e1001388.
27. Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25(14), 1754-1760.
28. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., et al. (2009). The sequence alignment/map format and SAMtools. Bioinformatics, 25(16), 2078-2079.
29. Li, H., & Homer, N. (2010). A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinformatics, 11(5), 473-483.
30. Mardis, E. R. (2008). Next-generation DNA sequencing methods. Annual Review of Genomics and Human Genetics, 9, 387-402.
31. Maricic, T., Whitten, M., & Paabo, S. (2010). Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS One, 5(11), e14004.
32. Mason, V. C., Li, G., Helgen, K. M., & Murphy, W. J. (2011). Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens. Genome Research, 21(10), 1695-1704.
33. McKelvey, K. S., & Schwartz, M. K. (2004). Genetic errors associated with population estimation using non-invasive molecular tagging: Problems and new solutions. Journal of Wildlife Management, 68, 439-448.
34. McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., et al. (2010). The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297-1303.
35. Miller, W., Hayes, V. M., Ratan, A., Petersen, D. C., Wittekindt, N. E., Miller, J., et al. (2011). Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). Proceedings of the National Academy of Sciences of the USA, 108(30), 12348-12353.
36. Miller, W., Schuster, S. C., Welch, A. J., Ratan, A., Bedoya-Reina, O. C., Zhao, F., et al. (2012). Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proceedings of the National Academy of Sciences of the USA, 109(36), E2382-E2390.
37. Nielsen, R., Paul, J. S., Albrechtsen, A., & Song, Y. S. (2011). Genotype and SNP calling from next-generation sequencing data. Nature Reviews Genetics, 12(6), 443-451.
38. Noonan, J. P., Coop, G., Kudaravalli, S., Smith, D., Krause, J., Alessi, J., et al. (2006). Sequencing and analysis of Neanderthal genomic DNA. Science, 314(5802), 1113-1118.
39. Ouborg, N. J., Pertoldi, C., Loeschcke, V., Bijlsma, R. K., & Hedrick, P. W. (2010). Conservation genetics in transition to conservation genomics. Trends in Genetics, 26(4), 177-187.
40. Parga, J. A., Sauther, M. L., Cuozzo, F. P., Jacky, I. A., & Lawler, R. R. (2012). Evaluating ring-tailed lemurs (Lemur catta) from southwestern Madagascar for a genetic population bottleneck. American Journal of Physical Anthropology, 147(1), 21-29.
41. Peery, M. Z., Kirby, R., Reid, B. N., Stoelting, R., Doucet-Beer, E., Robinson, S., et al. (2012). Reliability of genetic bottleneck tests for detecting recent population declines. Molecular Ecology, 21(14), 3403-3418.
42. Perry, G. H., Louis, E. E., Jr., Ratan, A., Bedoya-Reina, O. C., Burhans, R. C., Lei, R., et al. (2013). Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar. Proceedings of the National Academy of Sciences of the USA, 110(15), 5823-5828.
43. Perry, G. H., Marioni, J. C., Melsted, P., & Gilad, Y. (2010). Genomic-scale capture and sequencing of endogenous DNA from feces. Molecular Ecology, 19(24), 5332-5344.
44. Perry, G. H., Melsted, P., Marioni, J. C., Wang, Y., Bainer, R., Pickrell, J. K., et al. (2012a). Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Genome Research, 22(4), 602-610.
45. Perry, G. H., Reeves, D., Melsted, P., Ratan, A., Miller, W., Michelini, K., et al. (2012b). A Genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar. Genome Biology and Evolution, 4(2), 126-135.
46. Pompanon, F., Deagle, B. E., Symondson, W. O., Brown, D. S., Jarman, S. N., & Taberlet, P. (2012). Who is eating what: Diet assessment using next generation sequencing. Molecular Ecology, 21(8), 1931-1950.
47. Quemere, E., Amelot, X., Pierson, J., Crouau-Roy, B., & Chikhi, L. (2012). Genetic data suggest a natural prehuman origin of open habitats in northern Madagascar and question the deforestation narrative in this region. Proceedings of the National Academy of Sciences of the USA, 109(32), 13028-13033.
48. Shokralla, S., Spall, J. L., Gibson, J. F., & Hajibabaei, M. (2012). Next-generation sequencing technologies for environmental DNA research. Molecular Ecology, 21(8), 1794-1805.
49. St. John, J., & Quinn, T. W. (2008). Rapid capture of DNA targets. Biotechniques, 44(2), 259-264.
50. Steiner, C. C., Putnam, A. S., Hoeck, P. E. A., & Ryder, O. A. (2013). Conservation genomics of threatened animal species. Annual Review of Animal Biosciences, 1, 261-281.
51. Taberlet, P., Waits, L. P., & Luikart, G. (1999). Noninvasive genetic sampling: Look before you leap. Trends in Ecology & Evolution, 14(8), 323-327.
52. The 1000 Genomes Project Consortium. (2010). A map of human genome variation from population-scale sequencing. Nature, 467, 1061-1073.
53. Tung, J., Primus, A., Bouley, A. J., Severson, T. F., Alberts, S. C., & Wray, G. A. (2009). Evolution of a malaria resistance gene in wild primates. Nature, 460(7253), 388-391.
54. van Bortle, K., & Corces, V. G. (2012). Nuclear organization and genome function. Annual Review of Cell and Developmental Biology, 28, 163-187.
55. Wang, Z., Gerstein, M., & Snyder, M. (2009). RNA-Seq: A revolutionary tool for transcriptomics. Nature Reviews Genetics, 10(1), 57-63.
56. Zhao, S., Zheng, P., Dong, S., Zhan, X., Wu, Q., Guo, X., et al. (2013). Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation. Nature Genetics, 45(1), 67-71. 4.