Citation:

rspb.2019.0943

Name: Seawater carbonate chemistry and body size, change in allele frequency of Strongylocentrotus purpuratus larvae
Published: 2019
License: https://creativecommons.org/licenses/by/4.0/
Keywords: Animalia; Bottles or small containers/Aquaria (<20 L); Coast and continental shelf; Echinodermata; Gene expression (incl. proteomics); Laboratory experiment; North Pacific; Pelagos; Single species; Strongylocentrotus purpuratus; Temperate; Zooplankton

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Abstract:

Standing genetic variation is important for population persistence in extreme environmental conditions. While some species may have the capacity to adapt to predicted average future global change conditions, the ability to survive extreme events is largely unknown. We used single-generation selection experiments on hundreds of thousands of Strongylocentrotus purpuratus sea urchin larvae generated from wild-caught adults to identify adaptive genetic variation responsive to moderate (pH 8.0) and extreme (pH 7.5) low-pH conditions. Sequencing genomic DNA from pools of larvae, we identified consistent changes in allele frequencies across replicate cultures for each pH condition and observed increased linkage disequilibrium around selected loci, revealing selection on recombined standing genetic variation. We found that loci responding uniquely to either selection regime were at low starting allele frequencies while variants that responded to both pH conditions (11.6% of selected variants) started at high frequencies. Loci under selection performed functions related to energetics, pH tolerance, cell growth and actin/cytoskeleton dynamics. These results highlight that persistence in future conditions will require two classes of genetic variation: common, pH-responsive variants maintained by balancing selection in a heterogeneous environment, and rare variants, particularly for extreme conditions, that must be maintained by large population sizes.

Keyword(s):

Animalia; Bottles or small containers/Aquaria (<20 L); Coast and continental shelf; Echinodermata; Gene expression (incl. proteomics); Laboratory experiment; North Pacific; Pelagos; Single species; Strongylocentrotus purpuratus; Temperate; Zooplankton

Further details:

Gattuso, Jean-Pierre; Epitalon, Jean-Marie; Lavigne, Héloïse; Orr, James C; Gentili, Bernard; Hagens, Mathilde; Hofmann, Andreas; Mueller, Jens-Daniel; Proye, Aurélien; Rae, James; Soetaert, Karline (2019): seacarb: seawater carbonate chemistry with R. R package version 3.2.12. https://CRAN.R-project.org/package=seacarb

Project(s):

Ocean Acidification International Coordination Centre (OA-ICC)

Comment:

In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2019) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2020-02-17.

Parameter(s):

#	Name	Short Name	Unit	Principal Investigator	Method/Device	Comment
1	Type	Type		Pespeni, Melissa H		study
2	Species	Species		Pespeni, Melissa H
3	Registration number of species	Reg spec no		Pespeni, Melissa H
4	Uniform resource locator/link to reference	URL ref		Pespeni, Melissa H		WoRMS Aphia ID
5	Treatment	Treat		Pespeni, Melissa H
6	Identification	ID		Pespeni, Melissa H		Vessel
7	Body size	Body size	mm	Pespeni, Melissa H
8	Name	Name		Pespeni, Melissa H		Chromosome
9	Base pair size	Size b p	bp	Pespeni, Melissa H
10	Probability	Prob		Pespeni, Melissa H		from the Cochran-Mantel-Haenszel test
11	Name	Name		Pespeni, Melissa H		single nucleotide polymorphism
12	Change	Change		Pespeni, Melissa H		allele frequency from D1 to D7
13	Temperature, water	Temp	°C	Pespeni, Melissa H
14	Temperature, water, standard deviation	Temp std dev	±	Pespeni, Melissa H
15	Salinity	Sal		Pespeni, Melissa H
16	Salinity, standard deviation	Sal std dev	±	Pespeni, Melissa H
17	pH	pH		Pespeni, Melissa H		NBS scale
18	pH, standard deviation	pH std dev	±	Pespeni, Melissa H		NBS scale
19	Alkalinity, total	AT	µmol/kg	Pespeni, Melissa H
20	Alkalinity, total, standard deviation	AT std dev	±	Pespeni, Melissa H
21	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Pespeni, Melissa H
22	Partial pressure of carbon dioxide, standard deviation	pCO2 std dev	±	Pespeni, Melissa H
23	Carbonate system computation flag	CSC flag		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
24	pH	pH		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	total scale
25	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
26	Fugacity of carbon dioxide (water) at sea surface temperature (wet air)	fCO2water_SST_wet	µatm	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
27	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
28	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
29	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
30	Carbon, inorganic, dissolved	DIC	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
31	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
32	Calcite saturation state	Omega Cal		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)

License:

Creative Commons Attribution 4.0 International (CC-BY-4.0)

Status:

Curation Level: Enhanced curation (CurationLevelC)

Size:

5757 data points

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