Comparative population genomics in animals uncovers the determinants of genetic diversity

Nature

Volumn 515, Issue 7526, 2014, Pages 261-263

  Romiguier, J ^a,b   Gayral, P ^a,c   Ballenghien, M ^a   Bernard, A ^a   Cahais, V ^a   Chenuil, A ^d   Chiari, Y ^e   Dernat, R ^a   Duret, L ^f   Faivre, N ^a   Loire, E ^a   Lourenco, J M ^a   Nabholz, B ^a   Roux, C ^a,b   Tsagkogeorga, G ^a,g   Weber, A A T ^d   Weinert, L A ^a,h   Belkhir, K ^a   Bierne, N ^a   Glemin S ^a   Galtier, N ^a   more..

^a INSTITUT DES SCIENCES DE L EVOLUTION   (France)

^b UNIVERSITY OF LAUSANNE   (Switzerland)

^c UNIVERSITÉ DE TOURS   (France)

^d AVIGNON UNIVERSITÉ   (France)

^e UNIVERSITY OF SOUTH ALABAMA   (United States)

^f UNIVERSITÉ LYON 1   (France)

^g QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

^h UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ANIMAL; DNA; DOMESTICATION; GENETIC DIFFERENTIATION; GENOME; GENOMICS; LIFE HISTORY TRAIT; PARENTAL INVESTMENT; POLICY MAKING; POPULATION STRUCTURE; PREDICTION;

ANIMAL GENETICS; ARTICLE; BIODIVERSITY; CORRELATION ANALYSIS; ECOLOGICAL GENETICS; ENVIRONMENTAL FACTOR; GENETIC ASSOCIATION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOME; LIFE HISTORY TRAIT; MOLECULAR EVOLUTION; NEUTRAL GENE THEORY; NONHUMAN; POPULATION GENETICS; PREDICTIVE VALUE; PRIORITY JOURNAL; RNA SEQUENCE; WILDLIFE CONSERVATION; ANIMAL; COMPARATIVE STUDY; ECOLOGY; GENETICS; GENOMICS; PHYLOGENY;

ANIMALIA;

ANIMALS; ECOLOGY; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENETICS, POPULATION; GENOME; GENOMICS; PHYLOGENY;

EID: 84922016356     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature13685     Document Type: Article

References (25)

1. Lewontin, R. The Genetic Basis of Evolutionary Change (Columbia Univ. Press, 1974).
2. Leffler, E. M. et al. Revisiting an old riddle: what determines genetic diversity levels within species? PLoS Biol. 10, e1001388 (2012).
3. Keller, L. F. & Waller, D. M. Inbreeding effects in wild populations. Trends Ecol. Evol. 17, 19-23 (2002).
4. Reusch, T. B. H., Ehlers, A., Hämmerli, A. & Worm, B. Ecosystem recovery after climatic extremes enhanced by genotypic diversity. Proc. Natl Acad. Sci. USA 102, 2826-2831 (2005).
5. Hughes, A. R., Inouye, B. D., Johnson, M. T. J., Underwood, N. & Vellend, M. Ecological consequences of genetic diversity. Ecol. Lett. 11, 609-623 (2008).
6. Johnson, W. E. et al. Genetic restoration of the Florida panther. Science 329, 1641-1645 (2010).
7. Nair, P. Conservation genomics. Proc. Natl Acad. Sci. USA 111, 569 (2014).
8. Bazin, E., Glémin, S. & Galtier, N. Population size does not influence mitochondrial genetic diversity in animals. Science 312, 570-572 (2006).
9. Nabholz, B., Mauffrey, J.-F., Bazin, E., Galtier, N. & Glemin, S. Determination of mitochondrial genetic diversity in mammals. Genetics 178, 351-361 (2008).
10. Perry, G. et al. Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Genome Res. 22, 602-610 (2012).
11. Banks, S. C. et al. How does ecological disturbance influence genetic diversity? Trends Ecol. Evol. 28, 670-679 (2013).
12. Hewitt, G. The genetic legacy of the Quaternary ice ages. Nature 405, 907-913 (2000).
13. Ellegren, H. Genome sequencing and population genomics in non-model organisms. Trends Ecol. Evol. 29, 51-63 (2014).
14. Cahais, V. et al. Reference-free transcriptome assembly in non-model animals from next-generation sequencing data. Mol. Ecol. Resources 12, 834-845 (2012).
15. Tsagkogeorga, G., Cahais, V.&Galtier, N.Thepopulation genomics of a fast evolver: high levels of diversity, functional constraint, and molecular adaptation in the tunicate Ciona intestinalis. Genome Biol. Evol. 4, 740-749 (2012).
16. Gayral, P. et al. Reference-free population genomics from next-generation transcriptomedata and the vertebrate-invertebrate gap.PLoSGenet. 9, e1003457 (2013).
17. MacArthur, R. H. & Wilson, E. O. The Theory of Island Biogeography (Princeton Univ. Press, 1967).
18. Lynch, M. Evolution of the mutation rate. Trends Genet. 26, 345-352 (2010).
19. Ohta, T. Slightly deleterious mutant substitutions in evolution. Nature 246, 96-98 (1973).
20. Pinsky, M. L. et al. Unexpected patterns of fisheries collapse in the world's oceans. Proc. Natl Acad. Sci. USA 108, 8317-8322 (2011).
21. Gayral, P. et al. Next-generation sequencing of transcriptomes: a guide to RNA isolation in non-model animals. Mol. Ecol. Resources 11, 650-661 (2011).
22. Guéguen, L. et al. Bio11: efficient, extensible libraries and tools for molecular evolution. Mol. Biol. Evol. 30, 1745-1750 (2013).
23. Weir, B. S. & Cockerham, C. C. Estimating F-statistics for the analysis of population structure. Evolution 38, 1358-1370 (1984).
24. Philippe, H. et al. Phylogenomics revives traditional views on deep animal relationships. Curr. Biol. 19, 706-712 (2009).
25. Wilfert, L., Gadau, J.&Schmid-Hempel, P.Variationingenomic recombination rates among animal taxa and the case of social insects. Heredity 98, 189-197 (2007).