Dataset: Evolutionary and acclimatory shifts in gene expression of Eurytemora affinis copepods reared in saline and freshwater conditions during laboratory experiments from 2011-2014

Final no updates expectedDOI: 10.26008/1912/bco-dmo.883426.1Version 1 (2022-11-10)Dataset Type:Other Field ResultsDataset Type:experimental

Principal Investigator: Carol E. Lee (University of Wisconsin)

Student: Marijan Posavi (University of Wisconsin)

BCO-DMO Data Manager: Dana Stuart Gerlach (Woods Hole Oceanographic Institution)


Project: Evolutionary Responses to Global Changes in Salinity and Temperature (Evolutionary genomics of a copepod)


Abstract

To explore mechanisms of freshwater adaptation and distinguish between adaptive (evolutionary) and acclimatory (plastic) responses to salinity change, we examined genome‐wide patterns of gene expression between ancestral saline and derived freshwater populations of the Eurytemora affinis species complex, reared under two different common‐garden conditions (0 vs. 15 PSU). These data include the RNA-seq Illumina short paired end reads (101 base pairs) of 10 freshwater and 12 saline copepods Euryte...

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Study objectives
The goal of this study was to explore evolutionary shifts in gene expression between ancestral saline and freshwater invading populations of the Eurytemora affinis (copepod) species complex on a genome-wide scale. 

To explore mechanisms of freshwater adaptation and distinguish between adaptive (evolutionary) and acclimatory (plastic) responses to salinity change, laboratory experiments were conducted using both ancestral saline and derived freshwater populations of Eurytemora affinis.  Then RNA-seq data -- Illumina short paired-end (PE) reads (101 base pairs) of 10 freshwater and 12 saline E.affinis samples -- were used to answer the following questions:

  • (1)  What are the patterns of evolutionary shifts in gene expression between the ancestral saline and freshwater invading populations?
  • (2)  What are the plastic (acclimatory) changes in gene expression between salinities (0 PSU vs. 15 PSU conditions) within each of the saline and freshwater populations?
  • (3)  Are the magnitude and direction of plasticity in gene expression correlated with evolutionary responses?
  • (4)  Has plasticity in gene expression evolved following freshwater invasions?

Collection of ancestral populations
The copepods were collected using a plankton net mesh size of 50 μm in diameter, from a depth of 1-4 meters from near the shore. The freshwater copepods were collected in April-May 2006 by throwing the plankton net off the dock in Racine Harbor, Lake Michigan in Wisconsin, USA (42.729444 N, 87.778889 W). The saline copepods were collected by small boats near the shore in Baie de L'Isle Verte, St. Lawrence marsh, Quebec, Canada (48.003889 N, 69.425278 W) in May-June 2006.  Collected samples were transported to the laboratory where Eurytemora affinis individuals were identified and sampled under the microscope.

Laboratory cultures and experiments
Four inbred lines of Eurytemora affinis (two each from the two populations) were generated through full-sibling mating for 30 generations. Two independent saltwater inbred lines (SW1 and SW2) were derived from the ancestral saline population in Baie de L’Isle Verte (Canada) and reared at their native salinity of 15 PSU.  The two freshwater inbred lines (FW1 and FW2) were derived from the freshwater invading population in Racine Harbor (USA) and reared in Lake Michigan water (0 PSU, conductivity 300 μS/cm). In addition, reciprocal F1 crosses between freshwater and saline inbred lines were created and reared to test for allele-specific expression by comparing gene expression in parental lines and their F1 crosses.

Two replicate common-garden reaction norm experiments, each consisting of a 2 × 2 factorial design, were performed to compare patterns of the gene expression of the FW and SW inbred lines (see Materials and Methods in Posavi et al. 2020).  Total RNA from whole bodies of 50 copepods (25 females and 25 males) per sample was extracted using Trizol reagent (Ambion RNA) and Qiagen RNeasy Mini Kit for purification (Qiagen cat. no. 74104). Extracted and purified RNA samples were stored at -80 degrees Celsius until sequencing. The strand-specific Illumina RNA-seq libraries (Parkhomchuk et al., 2009) of polyA purified mRNA were constructed using the TruSeq RNA Sample Prep kit (Illumina). Three biological replicates per inbred line were sequenced using the Illumina HiSeq 2000 platform in the Institute for Genome Sciences at the University of Maryland School of Medicine and generated 101-bp-long paired-end read data. 

These data have important implications for understanding the evolutionary and physiological mechanisms of range expansions by some of the most widespread invaders in aquatic habitats. 

Problem report
One replicate of the FW1 inbred line was excluded because of bacterial infection

Additional information
~ Detailed methods, results, and figures can be found in Posavi et al. (2020) (see Related Publications section). 
~ The sequence data can be viewed under NCBI BioProject PRJNA278152 (see Related Datasets).


Related Datasets

IsDerivedFrom

Dataset: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA278152
University of Maryland School of Medicine. Eurytemora affinis Transcriptome or Gene expression. 2015/03. In: BioProject [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; 2011-. Available from: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA278152. NCBI:BioProject: PRJNA278152.
IsSupplementedBy

Dataset: https://i5k.nal.usda.gov/Eurytemora_affinis
Lee, C. (2020). Eurytemora affinis complex (Atlantic clade). i5k Workspace@NAL. https://i5k.nal.usda.gov/Eurytemora_affinis

Related Publications

Methods, Results

Posavi, M., Gulisija, D., Munro, J. B., Silva, J. C., & Lee, C. E. (2020). Rapid evolution of genome‐wide gene expression and plasticity during saline to freshwater invasions by the copepod Eurytemora affinis species complex. Molecular Ecology, 29(24), 4835–4856. Portico. https://doi.org/10.1111/mec.15681
Methods

Benjamini, Y., & Hochberg, Y. (2000). On the Adaptive Control of the False Discovery Rate in Multiple Testing With Independent Statistics. Journal of Educational and Behavioral Statistics, 25(1), 60–83. doi:10.3102/10769986025001060
Methods

De Wit, P., Pespeni, M. H., Ladner, J. T., Barshis, D. J., Seneca, F., Jaris, H., Therkildsen, N. O., Morikawa, M., & Palumbi, S. R. (2012). The simple fool’s guide to population genomics via RNA‐Seq: an introduction to high‐throughput sequencing data analysis. Molecular Ecology Resources, 12(6), 1058–1067. Portico. https://doi.org/10.1111/1755-0998.12003
Methods

Parkhomchuk, D., Borodina, T., Amstislavskiy, V., Banaru, M., Hallen, L., Krobitsch, S., Lehrach, H., & Soldatov, A. (2009). Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Research, 37(18), e123–e123. https://doi.org/10.1093/nar/gkp596
Methods

Robinson, M. D., & Oshlack, A. (2010). A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology, 11(3), R25. https://doi.org/10.1186/gb-2010-11-3-r25