Where's the ecology in molecular ecology?

Oikos

Volumn 118, Issue 11, 2009, Pages 1601-1609

  Johnson, Jerald B ^a   Peat, Scott M ^a   Adams, Byron J ^a  

^a BRIGHAM YOUNG UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ECOLOGICAL APPROACH; EVOLUTIONARY BIOLOGY; MOLECULAR ECOLOGY; THEORETICAL STUDY;

EID: 71949129650     PISSN: 00301299     EISSN: 16000706     Source Type: Journal    
DOI: 10.1111/j.1600-0706.2009.17557.x     Document Type: Review

References (79)

1. Ahern, R. G. et al. 2009. Phylogeography of a specialist insect, Adelges cooleyi: historical and contemporary processes shape the distribution of population genetic variation Mol. Ecol. 18 : 343 356.
2. Amos, B. 2000. Lessons form the history of light microscopy Nat. Cell Biol. 2 : E151 E152.
3. Antebi, A. 2007. Genetics of aging in Caenorhabditis elegans Plos Genet 3 : 1565 1571.
4. Avise, J. C. et al. 1987. Intraspecific phylogeography - the mitochondrial-DNA bridge between population-genetics and systematics Annu. Rev. Ecol. Syst. 18 : 489 522.
5. Balvanera, P. et al. 2006. Quantifying the evidence for biodiversity effects on ecosystem functioning and services Ecol. Lett. 9 : 1146 1156.
6. Barrett, J. E. et al. 2004. Variation in biogeochemistry and soil biodiversity across spatial scales in a polar desert ecosystem Ecology 85 : 3105 3118.
7. Barrett, J. E. et al. 2006a. Terrestrial ecosystem processes of Victoria Land, Antarctica Soil Biol. Biochem. 38 : 3019 3034.
8. Barrett, J. E. et al. 2006b. Co-variation in soil biodiversity and biogeochemistry in northern and southern Victoria Land, Antarctica Antarct. Sci. 18 : 535 548.
9. Barrett, J. E. et al. 2008. Decline in a dominant invertebrate species contributes to altered carbon cycling in a low-diversity soil ecosystem Global Change Biol. 14 : 1734 1744.
10. Beebee, T. Rowe, G. 2004. An introduction to molecular ecology. Oxford Univ. Press.
11. Bohannan, B. J. M. Hughes, J. 2003. New approaches to analyzing microbial biodiversity data Curr. Opin. Microbiol. 6 : 282 287.
12. Brooks, D. R. McLennan, D. A. 1991. Phylogeny, ecology, and behavior: a research program in comparative biology. Univ. of Chicago Press.
13. Brooks, D. R. McLennan, D. A. 2002. The nature of diversity: an evolutionary voyage of discovery. Univ. of Chicago Press.
14. Burke, T. et al. 1992. Editorial Mol. Ecol. 1 : 1.
15. Caswell, H. 2001. Matrix population models: construction, analysis and interpretation. Sinauer.
16. Caswell-Chen, E. P. Caswell, H. 2007. Evolutionary ecology of aging in Caenorhabditis elegans: nurture and nature J. Nematol. 39 : 86 87.
17. Chen, J. et al. 2006. The ecology and biodemography of Caenorhabditis elegans Exp. Gerontol. 41 : 1059 1065.
18. Cohan, F. M. Perry, E. B. 2007. A systematics for discovering the fundamental units of bacterial diversity Curr. Biol. 17 : R373 R386.
19. Conner, J. K. Hartl, D. L. 2004. A primer of ecological genetics. Sinauer.
20. Cornwell, W. K. et al. 2008. Plant species traits are the predominant control on litter decomposition rates within biomes worldwide Ecol. Lett. 11 : 1065 1071.
21. Crandall, K. A. et al. 2000. Considering evolutionary processes in conservation biology Trends Ecol. Evol. 15 : 290 295.
22. Curran, S. P. Ruvkun, G. 2007. Lifespan regulation by evolutionarily conserved genes essential for viability. Plos Genet 3.
23. Dingemanse, N. J. et al. 2003. Natal dispersal and personalities in great tits (Parus major) Proc. R. Soc. Lond. B 270 : 741 747.
24. Doran, P. T. et al. 2002. Antarctic climate cooling and terrestrial ecosystem response Nature 415 : 517 520.
25. Drummond, A. J. et al. 2005. Bayesian coalescent inference of past population dynamics from molecular sequences Mol. Biol. Evol. 22 : 1185 1192.
26. Farrell, L. E. et al. 2000. Dietary separation of sympatric carnivores identified by molecular analysis of scats Mol. Ecol. 9 : 1583 1590.
27. Fedriani, J. M. Kohn, M. H. 2001. Genotyping feces links individuals to their diet Ecol. Lett. 4 : 477 483.
28. Futuyma, D. J. 2005. Evolution. Sinauer.
29. Green, J. L. Plotkin, J. B. 2007. A statistical theory for sampling species abundances Ecol. Lett. 10 : 1037 1045.
30. Guralnick, R. 2006. The legacy of past climate and landscape change on species' current experienced climate and elevation ranges across latitude: a multispecies study utilizing mammals in western North America Global Ecol. Biogeogr. 15 : 505 518.
31. Gutteling, E. W. et al. 2007. Environmental influence on the genetic correlations between life-history traits in Caenorhabditis elegans Heredity 98 : 206 213.
32. Hamilton, B. et al. 2005. A systematic RNAi screen for longevity genes in C. elegans Genes Dev. 19 : 1544 1555.
33. Harris, M. A. et al. 2008. The Gene Ontology project in 2008 Nucleic Acids Res. 36 : D440 D444.
34. Hayes, B. J. et al. 2003. Novel multilocus measure of linkage disequilibrium to estimate past effective population size Genome Res. 13 : 635 643.
35. Hebert, P. D. N. et al. 2004. Ten species in one: DNA barcoding reveals cryptic species in the Neotropical skipper butterfly Astraptes fulgerator Proc. Natl Acad. Sci. USA 101 : 14812 14817.
36. Hooper, D. U. et al. 2000. Interactions between aboveground and belowground biodiversity in terrestrial ecosystems: patterns, mechanisms and feedback BioScience 50 : 1049 1061.
37. Hooper, D. U. et al. 2005. Effects of biodiversity on ecosystem functioning: a consensus of current knowledge Ecol. Monogr. 75 : 3 35.
38. Hung, E. H. C. 2006. Beyond Kuhn: scientific explanation, theory structure, incommensurability and physical necessity. Ashgate Pub.
39. Jeyasingh, P. D. Weider, L. J. 2007. Fundamental links between genes and elements: evolutionary implications of ecological stoichiometry Mol. Ecol. 16 : 4649 4661.
40. Kanehisa, M. Goto, S. 2000. KEGG: Kyoto encyclopedia of genes and genomes Nucl. Acids Res. 28 : 27 30.
41. Kohn, M. H. et al. 1999. Estimating population size by genotyping faeces Proc. R. Soc. Lond. B 266 : 657 663.
42. Kuhn, T. S. 1962. The structure of scientific revolutions. Univ. of Chicago Press.
43. Kuhner, M. K. et al. 1998. Maximum likelihood estimation of population growth rates based on the coalescent Genetics 149 : 429 434.
44. Lapointe, F. J. Rissler, L. J. 2005. Congruence, consensus, and the comparative phylogeography of codistributed species in California Am. Nat. 166 : 290 299.
45. Lowe, A. et al. 2004. Ecological genetics: design, analysis and application. Blackwell.
46. Lozupone, C. A. Knight, R. 2008. Species divergence and the measurement of microbial diversity FEMS Microbiol. Rev. 32 : 557 578.
47. Lukoschek, V. et al. 2007. Phylogeography of the olive sea snake, Aipysurus laevis (Hydrophiinae) indicates Pleistocene range expansion around northern Australia but low contemporary gene flow Mol. Ecol. 16 : 3406 3422.
48. May, R. 1999. Unanswered questions in ecology Philos. Trans. R. Soc. Lond. B 354 : 1951 1959.
49. Mills, L. S. et al. 2000. Estimating animal abundance using noninvasive DNA sampling: promise and pitfalls Ecol. Appl. 10 : 283 294.
50. Minin, V. N. et al. 2008. Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics Mol. Biol. Evol. 25 : 1459 1471.
51. Moritz, C. 1994. Defining evolutionarily-significant-units for conservation Trends Ecol. Evol. 9 : 373 375.
52. Moyer, G. R. et al. 2005. Genetic and ecological dynamics of species replacement in an arid-land river system Mol. Ecol. 14 : 1263 1273.
53. Niklaus, P. A. et al. 2006. Effects of plant species diversity and composition on nitrogen cycling and the trace gas balance of soils Plant Soil 282 : 83 98.
54. Noss, R. F. 1990. Indicators for monitoring biodiversity - a hierarchical approach Conserv. Biol. 4 : 355 364.
55. Paun, O. et al. 2008. Historical divergence vs contemporary gene flow: evolutionary history of the calcicole Ranunculus alpestris group (Ranunculaceae) in the European Alps and the Carpathians Mol. Ecol. 17 : 4263 4275.
56. Piggott, M. P. Taylor, A. C. 2003. Remote collection of animal DNA and its applications in conservation management and understanding the population biology of rare and cryptic species Wildlife Res. 30 : 1 13.
57. Purugganan, M. Gibson, G. 2003. Merging ecology, molecular evolution, and functional genetics Mol. Ecol. 12 : 1109 1112.
58. Queller, D. C. et al. 1993. Microsatellites and kinship Trends Ecol. Evol. 8 : 285 288.
59. Reed, S. C. et al. 2008. Tree species control rates of free-living nitrogen fixation in a tropical rain forest Ecology 89 : 2924 2934.
60. Rhee, S. Y. et al. 2008. Use and misuse of the gene ontology annotations Nat. Rev. Genet. 9 : 509 515.
61. Ricklefs, R. E. Miller, G. L. 1999. Ecology. W. H. Freeman.
62. Rieseberg, L. Smith, H. 2000a. Molecular ecology in the year 2000 Mol. Ecol. 9 : i v.
63. Rieseberg, L. Smith, H. 2000b. Molecular ecology notes: announcement of sister journal to Molecular Ecology Mol. Ecol. 9 : U1 U1.
64. Rieseberg, L. Smith, H. 2001. Molecular ecology in the year 2001 Mol. Ecol. 10 : U1 U3.
65. Rissler, L. J. Apodaca, J. J. 2007. Adding more ecology into species delimitation: ecological niche models and phylogeography help define cryptic species in the black salamander (Aneides flavipunctatus) Syst. Biol. 56 : 924 942.
66. Rissler, L. J. et al. 2006. Phylogeographic lineages and species comparisons in conservation analyses: a case study of California herpetofauna Am. Nat. 167 : 655 666.
67. Ross, K. G. 2001. Molecular ecology of social behaviour: analyses of breeding systems and genetic structure Mol. Ecol. 10 : 265 284.
68. Ryder, O. A. 1986. Species conservation and systematics: the dilemma of subspecies Trends Ecol. Evol. 1 : 9 10.
69. Sakai, A. K. et al. 2001. The population biology of invasive species Annu. Rev. Ecol. Syst. 32 : 305 332.
70. Sih, A. et al. 2004. Behavioral syndromes: an integrative approach Q. Rev. Biol. 79 : 241 277.
71. Song, H. et al. 2008. Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified Proc. Natl Acad. Sci. USA 105 : 13486 13491.
72. Sterner, R. W. Elser, J. J. 2002. Ecological stoichiometry: the biology of elements from molecules to the biosphere. Princeton Univ. Press.
73. Travers, S. E. et al. 2007. Ecological genomics: making the leap from model systems in the lab to native populations in the field Front. Ecol. Environ. 5 : 19 24.
74. Vasco, D. A. 2008. A fast and reliable computational method for estimating population genetic parameters Genetics 179 : 951 963.
75. Victoriano, P. F. et al. 2008. Comparative phylogeography of codistributed species of Chilean Liolaemus (Squamata: Tropiduridae) from the central-southern Andean range Mol. Ecol. 17 : 2397 2416.
76. Walker, F. M. et al. 2006. Genotyping of "captured" hairs reveals burrow-use and ranging behavior of southern hairy-nosed wombats J. Mammal. 87 : 690 699.
77. Waples, R. S. 1991. Pacific salmon, Oncorhynchus spp., and the definition of 'species' under the endangered species act Mar. Fish. Rev. 53 : 11 22.
78. Williams, G. C. 1957. Pleiotropy, natural-selection and the evolution of senescence Evolution 11 : 398 411.
79. Zak, D. R. et al. 2006. A molecular dawn for biogeochemistry Trends Ecol. Evol. 21 : 288 295.