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| Status |
Public on Jan 01, 2012 |
| Title |
Daphnia ecotypes fed lab versus natural resources |
| Platform organism |
Daphnia pulex |
| Sample organisms |
Daphnia pulex; Daphnia pulicaria |
| Experiment type |
Expression profiling by array
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| Summary |
Consumer-resource interactions are a central issue in evolutionary and community ecology because they play important roles in selection and population regulation. Most consumers encounter resource variation at multiple scales, and respond through phenotypic plasticity in the short term or evolutionary divergence in the long term. The key traits for these responses may influence resource acquisition, assimilation and/or allocation. To identify candidate genes, we experimentally assayed genome-wide gene expression in pond and lake Daphnia ecotypes exposed to alternate resource environments. One was a simple, high-quality laboratory diet, Ankistrodesmus falcatus. The other was the complex natural seston from a large lake. In temporary ponds, Daphnia generally experience high-quality, abundant resources, whereas lakes provide low-quality, seasonally shifting resources that are chronically limiting. For both ecotypes, we used replicate clones drawn from a number of separate populations.
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| Overall design |
We compared gene expression in whole Daphnia pulex that had been raised in the lab for 10 days, and then exposed to alternate resource environments for 24 hours. One resource environment was a 24 hour continuation of the lab resource, a satiating level of Ankistrodesmus falcatus. The alternate environment was the natural seston present in the epilimnion of Lake Murray, South Carolina. Two ecotypes were analyzed, one adapted to large lakes, and one adapted to temporary ponds. For each ecotype, eight replicate clones were used. Clones of the lake ecotype were isolated from eight independent lakes, clones of the pond ecotype were isolated from six different ponds. The total number of arrays is 16 (8 replicate clones x 2 ecotypes) x 2 resource environments). Total RNA was extracted from eight whole organisms pooled together. Pools were then converted to cDNA and labelled with a single round of amplification. For array hybridizations, samples from the two resource environments were paired for each clone, and dyes were swapped across clones.
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| Contributor(s) |
Dudycha JL, Deitz KC, Brandon CS |
| Citation(s) |
22423327 |
| Submission date |
Jul 27, 2011 |
| Last update date |
Jun 25, 2012 |
| Contact name |
Jeffry L. Dudycha |
| E-mail(s) |
dudycha@biol.sc.edu
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| Organization name |
University of South Carolina
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| Department |
Biological Sciences
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| Street address |
715 Sumter Street
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| City |
Columbia |
| State/province |
SC |
| ZIP/Postal code |
29208 |
| Country |
USA |
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| Platforms (1) |
| GPL13280 |
Indiana University/CGB-Daphnia-10K-Gen 3 |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA146335 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE31001_RAW.tar |
17.7 Mb |
(http)(custom) |
TAR (of GPR) |
| GSE31001_normalized.txt.gz |
957.7 Kb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
| Processed data are available on Series record |
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