Citation:

PANGAEA.937391

Name: Seawater carbonate chemistry and bioinformatic quality statistics
Published: 2021-10-15
License: https://creativecommons.org/licenses/by/4.0/
Keywords: Animalia; Benthic animals; Benthos; Bottles or small containers/Aquaria (<20 L); Coast and continental shelf; Crassostrea gigas; Gene expression (incl. proteomics); Laboratory experiment; Mollusca; North Pacific; Single species; Temperate

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Abstract:

The adaptive capacity of marine calcifiers to ocean acidification (OA) is a topic of great interest to evolutionary biologists and ecologists. Previous studies have provided evidence to suggest that larval resilience to high pCO2 seawater for these species is a trait with a genetic basis and variability in natural populations. To date, however, it remains unclear how the selective effects of OA occur within the context of complex genetic interactions underpinning larval development in many of the most vulnerable taxa. Here we evaluated phenotypic and genetic changes during larval development of Pacific oysters (Crassostrea gigas) reared in ambient (400 µatm) and high (1600 µatm) pCO2 conditions, both in domesticated and naturalized 'wild' oysters from the Pacific Northwest, USA. Using pooled DNA samples, we determined changes in allele frequencies across larval development, from early “D-stage” larvae to metamorphosed juveniles (spat), in both groups and environments. Domesticated larvae had 26% fewer loci with changing allele frequencies across developmental stages and < 50% as many loci affected by acidified culture conditions, compared to larvae from wild brood stock. Functional enrichment analyses of genetic markers with significant changes in allele frequency revealed that the structure and function of cellular membranes were disproportionately affected by high pCO2 conditions in both groups. These results indicate the potential for a rapid adaptive response of oyster populations to OA conditions; however, underlying genetic changes associated with larval development differ between these wild and domesticated oyster stocks and influence their adaptive responses to OA conditions.

Keyword(s):

Animalia; Benthic animals; Benthos; Bottles or small containers/Aquaria (<20 L); Coast and continental shelf; Crassostrea gigas; Gene expression (incl. proteomics); Laboratory experiment; Mollusca; North Pacific; Single species; Temperate

Related to:

Durland, Evan; de Wit, Pierre; Meyer, Eli; Langdon, Chris (2021): Larval development in the Pacific oyster and the impacts of ocean acidification: Differential genetic effects in wild and domesticated stocks. Evolutionary Applications, 14(9), 2258-2272, https://doi.org/10.1111/eva.13289

Source:

Durland, Evan; de Wit, Pierre; Meyer, Eli; Langdon, Chris (2021): Full output of functional enrichment analyses and gene annotations for membrane functions [dataset]. Durlan_etal_2021_Raw_Data.rar

Further details:

Gattuso, Jean-Pierre; Epitalon, Jean-Marie; Lavigne, Héloïse; Orr, James (2021): seacarb: seawater carbonate chemistry with R. R package version 3.2.16. https://cran.r-project.org/web/packages/seacarb/index.html

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, 2021) 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 2021-10-14.

Parameter(s):

#	Name	Short Name	Unit	Principal Investigator	Method/Device	Comment
1	Type	Type		Durland, Evan		study
2	Species	Species		Durland, Evan
3	Registration number of species	Reg spec no		Durland, Evan
4	Uniform resource locator/link to reference	URL ref		Durland, Evan		WoRMS Aphia ID
5	Group	Group		Durland, Evan
6	Treatment	Treat		Durland, Evan
7	Age	Age	days	Durland, Evan
8	Replicate	Repl		Durland, Evan
9	Reads	Reads	#	Durland, Evan		Raw
10	Reads	Reads	#	Durland, Evan		Quality
11	Reads	Reads	#	Durland, Evan		matched to illumina adaptor seq
12	Reads	Reads	#	Durland, Evan		Quality and clean
13	Reads	Reads	#	Durland, Evan		Mapped
14	Percentage	Perc	%	Durland, Evan		mapped
15	Ratio	Ratio		Durland, Evan		Avg hits/ matched read
16	Reads	Reads	#	Durland, Evan		Raw mappings
17	Reads	Reads	#	Durland, Evan		>=1 match
18	Reads	Reads	#	Durland, Evan		Weak match
19	Reads	Reads	#	Durland, Evan		Ambiguous match
20	Reads	Reads	#	Durland, Evan		Unique remaining
21	Reads	Reads	#	Durland, Evan		Net mapped loci
22	Temperature, water	Temp	°C	Durland, Evan
23	Temperature, water, standard error	T std e	±	Durland, Evan
24	Salinity	Sal		Durland, Evan
25	Salinity, standard error	Sal std e	±	Durland, Evan
26	Alkalinity, total	AT	µmol/kg	Durland, Evan
27	Alkalinity, total, standard error	AT std e	±	Durland, Evan
28	Carbon, inorganic, dissolved	DIC	µmol/kg	Durland, Evan
29	Carbon, inorganic, dissolved, standard error	DIC std e	±	Durland, Evan
30	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Durland, Evan
31	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air), standard error	pCO2water_SST_wet std e	±	Durland, Evan
32	Bicarbonate ion	[HCO3]-	µmol/kg	Durland, Evan
33	Bicarbonate ion, standard error	[HCO3]- std e	±	Durland, Evan
34	Carbonate ion	[CO3]2-	µmol/kg	Durland, Evan
35	Carbonate ion, standard error	[CO3]2- std e	±	Durland, Evan
36	pH	pH		Durland, Evan		total scale
37	pH, standard error	pH std e	±	Durland, Evan		total scale
38	Calcite saturation state	Omega Cal		Durland, Evan
39	Calcite saturation state, standard error	Omega Cal std e	±	Durland, Evan
40	Aragonite saturation state	Omega Arg		Durland, Evan
41	Aragonite saturation state, standard error	Omega Arg std e	±	Durland, Evan
42	Carbonate system computation flag	CSC flag		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
43	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
44	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)
45	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)
46	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
47	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
48	Alkalinity, total	AT	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
49	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
50	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:

1950 data points

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