Can clustering in genotype space reveal “Niches”?

American Naturalist

Volumn 187, Issue 1, 2015, Pages 130-135

  D'Andrea, Rafael ^a   Ostling, Annette ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Abundance correla tions; Community assembly; Immigration; Mutation; Neutral theory; Selection

Indexed keywords

BIOTA; CLUSTER ANALYSIS; COMPUTER SIMULATION; GENETICS; GENOTYPE; MARKOV CHAIN; MICROBIAL CONSORTIUM; POINT MUTATION; POPULATION GENETICS; THEORETICAL MODEL;

BIOTA; CLUSTER ANALYSIS; COMPUTER SIMULATION; GENETICS, POPULATION; GENOTYPE; MICROBIAL CONSORTIA; MODELS, THEORETICAL; POINT MUTATION; STOCHASTIC PROCESSES;

EID: 84951276372     PISSN: 00030147     EISSN: None     Source Type: Journal    
DOI: 10.1086/684116     Document Type: Note

References (16)

1. Adler, P. B., J. HilleRisLambers, and J. M. Levine. 2007. A niche for neutrality. Ecology Letters 10:95-104.
2. Akey, J. M., M. A. Eberle, M. J. Rieder, C. S. Carlson, M. D. Shriver, D. A. Nickerson, and L. Kruglyak. 2006. Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biology 2:e286.
3. Cavalli-Sforza, L. L. 1966. Population structure and human evolu-tion. Proceedings of the Royal Society B: Biological Sciences 164: 362-379.
4. Czernilofsky, A. P., C. G. Kurland, and G. Stöffler. 1975. 30S ribo-somal proteins associated with the 30-terminus of 16S RNA. FEBS Letters 58:281-284.
5. Funkhouser, L. J., and S. R. Bordenstein. 2013. Mom knows best: the universality of maternal microbial transmission. PloS Biology 11: 1-9.
6. Holt, R. 2006. Emergent neutrality. Trends in Ecology and Evolution 21:531-533.
7. Houchmandzadeh, B., and M. Vallade. 2003. Clustering in neutral ecology. Physical Review E 68:061912.
8. Jeraldo, P., M. Sipos, N. Chia, J. M. Brulc, A. S. Dhillon, M. E. Konkel, C. L. Larson, et al. 2012. Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal micro-biomes. Proceedings of the National Academy of Sciences of the USA 109:9692-9698.
9. Kohl, K. D., A. Stengel, and M. D. Dearing. 2015. Inoculation of tannin-degrading bacteria into novel hosts increases performance on tannin-rich diets. Environmental Microbiology. doi:10.1111/1462-2920.12841.
10. Lauring, A. S., J. Frydman, and R. Andino. 2013. The role of muta-tional robustness in RNA virus evolution. Nature Reviews Micro-biology 11:327-336.
11. Levy, R., and E. Borenstein. 2013. Metabolic modeling of species in-teraction in the human microbiome elucidates community-level assembly rules. Proceedings of the National Academy of Sciences of the USA 110:12804-12809.
12. Ochman, H., S. Elwyn, and N. A. Moran. 1999. Calibrating bacterial evolution. Proceedings of the National Academy of Sciences of the USA 96:12638-12643.
13. Seedorf, H., N. W. Griffin, V. K. Ridaura, A. Reyes, J. Cheng, F. E. Rey, M. I. Smith, et al. 2014. Bacteria from diverse habitats colo-nize and compete in the mouse gut. Cell 159:253-266.
14. Vallade, M., and B. Houchmandzadeh. 2003. Analytical solution of a neutral model of biodiversity. Physical Review E 68:061902.
15. Wilke, C. O. 2005. Quasispecies theory in the context of population genetics. BMC Evolutionary Biology 5:44.
16. Wilson, M. K, and C. A. E. Briggs. 1955. The normal flora of the bovine rumen. II. Quantitative bacteriological studies. Journal of Applied Bacteriology 18:294-306.