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Durland, Evan; de Wit, Pierre; Meyer, Eli; Langdon, Chris (2021): Seawater carbonate chemistry and bioinformatic quality statistics [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.937391

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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. 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
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):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
TypeTypeDurland, Evanstudy
SpeciesSpeciesDurland, Evan
Registration number of speciesReg spec noDurland, Evan
Uniform resource locator/link to referenceURL refDurland, EvanWoRMS Aphia ID
GroupGroupDurland, Evan
TreatmentTreatDurland, Evan
AgeAgedaysDurland, Evan
ReplicateReplDurland, Evan
ReadsReads#Durland, EvanRaw
10 ReadsReads#Durland, EvanQuality
11 ReadsReads#Durland, Evanmatched to illumina adaptor seq
12 ReadsReads#Durland, EvanQuality and clean
13 ReadsReads#Durland, EvanMapped
14 PercentagePerc%Durland, Evanmapped
15 RatioRatioDurland, EvanAvg hits/ matched read
16 ReadsReads#Durland, EvanRaw mappings
17 ReadsReads#Durland, Evan>=1 match
18 ReadsReads#Durland, EvanWeak match
19 ReadsReads#Durland, EvanAmbiguous match
20 ReadsReads#Durland, EvanUnique remaining
21 ReadsReads#Durland, EvanNet mapped loci
22 Temperature, waterTemp°CDurland, Evan
23 Temperature, water, standard errorT std e±Durland, Evan
24 SalinitySalDurland, Evan
25 Salinity, standard errorSal std e±Durland, Evan
26 Alkalinity, totalATµmol/kgDurland, Evan
27 Alkalinity, total, standard errorAT std e±Durland, Evan
28 Carbon, inorganic, dissolvedDICµmol/kgDurland, Evan
29 Carbon, inorganic, dissolved, standard errorDIC std e±Durland, Evan
30 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmDurland, Evan
31 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air), standard errorpCO2water_SST_wet std e±Durland, Evan
32 Bicarbonate ion[HCO3]-µmol/kgDurland, Evan
33 Bicarbonate ion, standard error[HCO3]- std e±Durland, Evan
34 Carbonate ion[CO3]2-µmol/kgDurland, Evan
35 Carbonate ion, standard error[CO3]2- std e±Durland, Evan
36 pHpHDurland, Evantotal scale
37 pH, standard errorpH std e±Durland, Evantotal scale
38 Calcite saturation stateOmega CalDurland, Evan
39 Calcite saturation state, standard errorOmega Cal std e±Durland, Evan
40 Aragonite saturation stateOmega ArgDurland, Evan
41 Aragonite saturation state, standard errorOmega Arg std e±Durland, Evan
42 Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
43 Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
44 Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
45 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
46 Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
47 Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
48 Alkalinity, totalATµmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
49 Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
50 Calcite saturation stateOmega CalYang, YanCalculated using seacarb after Nisumaa et al. (2010)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
1950 data points

Data

Download dataset as tab-delimited text — use the following character encoding:


Type
(study)

Species

Reg spec no

URL ref
(WoRMS Aphia ID)

Group

Treat

Age [days]

Repl

Reads [#]
(Raw)
10 
Reads [#]
(Quality)
11 
Reads [#]
(matched to illumina adaptor seq)
12 
Reads [#]
(Quality and clean)
13 
Reads [#]
(Mapped)
14 
Perc [%]
(mapped)
15 
Ratio
(Avg hits/ matched read)
16 
Reads [#]
(Raw mappings)
17 
Reads [#]
(>=1 match)
18 
Reads [#]
(Weak match)
19 
Reads [#]
(Ambiguous match)
20 
Reads [#]
(Unique remaining)
21 
Reads [#]
(Net mapped loci)
22 
Temp [°C]
23 
T std e [±]
24 
Sal
25 
Sal std e [±]
26 
AT [µmol/kg]
27 
AT std e [±]
28 
DIC [µmol/kg]
29 
DIC std e [±]
30 
pCO2water_SST_wet [µatm]
31 
pCO2water_SST_wet std e [±]
32 
[HCO3]- [µmol/kg]
33 
[HCO3]- std e [±]
34 
[CO3]2- [µmol/kg]
35 
[CO3]2- std e [±]
36 
pH
(total scale)
37 
pH std e [±]
(total scale)
38 
Omega Cal
39 
Omega Cal std e [±]
40 
Omega Arg
41 
Omega Arg std e [±]
42 
CSC flag
43 
CO2 [µmol/kg]
44 
fCO2water_SST_wet [µatm]
45 
pCO2water_SST_wet [µatm]
46 
[HCO3]- [µmol/kg]
47 
[CO3]2- [µmol/kg]
48 
AT [µmol/kg]
49 
Omega Arg
50 
Omega Cal
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laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgMBPAmbient253551893351331415574349774018609920.5320555562.1339553061559796497069100137555842116177324.50.8629.80.27224934206950651215.1191172139.332.17.890.133.430.792.280.53924.56845.67848.381959.72112.862233.431.842.82
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laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgMBPAmbient2245226179518245692207509024930627300.6016856942.02617216925338918889451478767105512428536524.50.8629.80.27224934206950651215.1191172139.332.17.890.133.430.792.280.53924.56845.67848.381959.72112.862233.431.842.82
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgMBPAmbient2255068494502098645763497522331613630.6354213672.05648432926393918767451587284105210729686124.50.8629.80.27224934206950651215.1191172139.332.17.890.133.430.792.280.53924.56845.67848.381959.72112.862233.431.842.82
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgMBPHigh pCO2215348346528852922769526576032621270.6194978502.0968341162692901940230169556299733923114924.41.0230.50.262294312260181791364.321461761.010.37.480.091.500.251.000.16960.882099.552106.282146.7454.622278.540.891.36
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laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgMBPHigh pCO22333936793345630101380324425017723590.5463077752.053631239147773249647788725559047721361724.41.0230.50.262294312260181791364.321461761.010.37.480.091.500.251.000.16960.882099.552106.282146.7454.622278.540.891.36
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgMBPHigh pCO2248565784847653838603843793555188820.6540559982.1111638519454849116412762889090165940131230424.41.0230.50.262294312260181791364.321461761.010.37.480.091.500.251.000.16960.882099.552106.282146.7454.622278.540.891.36
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgMBPHigh pCO2255606621554127440282550099231776890.5776574482.1467925792684745825894173128395346218608424.41.0230.50.262294312260181791364.321461761.010.37.480.091.500.251.000.16960.882099.552106.282146.7454.622278.540.891.36
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgMBPHigh pCO22212929883290464542745286190017374130.6070837561.993462043142695452092381650161045328767524.41.0230.50.262294312260181791364.321461761.010.37.480.091.500.251.000.16960.882099.552106.282146.7454.622278.540.891.36
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgMBPHigh pCO22226158540607994836990604295837613220.6224306042.037637542309351011354801826738126677230357824.41.0230.50.262294312260181791364.321461761.010.37.480.091.500.251.000.16960.882099.552106.282146.7454.622278.540.891.36
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgMBPHigh pCO222351062315056841125250493159130816730.6248841402.00617375625439449101981467920107602427855624.41.0230.50.262294312260181791364.321461761.010.37.480.091.500.251.000.16960.882099.552106.282146.7454.622278.540.891.36
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgMBPHigh pCO22245474384542588256657536922533188550.6181255211.976548697270593410225011524820118111436903924.41.0230.50.262294312260181791364.321461761.010.37.480.091.500.251.000.16960.882099.552106.282146.7454.622278.540.891.36
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgMBPHigh pCO22255453414538547472529531294532369950.6092656712.02655417526836199369431579342110427729517824.41.0230.50.262294312260181791364.321461761.010.37.480.091.500.251.000.16960.882099.552106.282146.7454.622278.540.891.36
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgWillapaAmbient211212594711990480400111195046979529530.6654929612.1116763388657172323538094162912240881134370924.50.9029.82.27226730208356640203.1192277142.029.77.890.123.500.732.330.48923.95824.85827.491982.87118.372269.081.932.95
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgWillapaAmbient222229377219921940660215855912958260.6003199362.102714863107068638470266938140130516220324.50.9029.82.27226730208356640203.1192277142.029.77.890.123.500.732.330.48923.95824.85827.491982.87118.372269.081.932.95
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgWillapaAmbient234396436435011017557433255325365050.5854527342.0852654792089392753353128972879966421475024.50.9029.82.27226730208356640203.1192277142.029.77.890.123.500.732.330.48923.95824.85827.491982.87118.372269.081.932.95
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgWillapaAmbient24235730323311818366232281514210600.6117835472.102989325118530740107074408444122319318924.50.9029.82.27226730208356640203.1192277142.029.77.890.123.500.732.330.48923.95824.85827.491982.87118.372269.081.932.95
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgWillapaAmbient253912891385857384178377439513237290.3507128962.132817945111303634474371315239988420015824.50.9029.82.27226730208356640203.1192277142.029.77.890.123.500.732.330.48923.95824.85827.491982.87118.372269.081.932.95
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgWillapaAmbient2218761300866623090015857621550744310.5916865422.0710494511425085413979472595811165504327489424.50.9029.82.27226730208356640203.1192277142.029.77.890.123.500.732.330.48923.95824.85827.491982.87118.372269.081.932.95
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgWillapaAmbient2224693999464063052350458828027633620.6022653372.0255761662288543804410133768495085928436224.50.9029.82.27226730208356640203.1192277142.029.77.890.123.500.732.330.48923.95824.85827.491982.87118.372269.081.932.95
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgWillapaAmbient2238970549888645650614883584256143300.6354040742.0411427594464636816289062761730188463839645024.50.9029.82.27226730208356640203.1192277142.029.77.890.123.500.732.330.48923.95824.85827.491982.87118.372269.081.932.95
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laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgWillapaHigh pCO2214873652481699535516478147930952050.6473321332.03629191725497979280021511424103837335494124.31.0030.50.362304232270241790326.821562361.19.27.480.081.500.221.000.15961.002096.762103.492167.2354.762299.120.891.37
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgWillapaHigh pCO2226753058667597742073663390441801110.6301132792.038506196345549212414482053659140183328288824.31.0030.50.362304232270241790326.821562361.19.27.480.081.500.221.000.15961.002096.762103.492167.2354.762299.120.891.37
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgWillapaHigh pCO2234961648490219374251482794221967930.4550164442.1747738601880854526028123936764148714649924.31.0030.50.362304232270241790326.821562361.19.27.480.081.500.221.000.15961.002096.762103.492167.2354.762299.120.891.37
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgWillapaHigh pCO2244476514442980139608439019328037510.6386395772.1259495142335600794981149246984313122274024.31.0030.50.362304232270241790326.821562361.19.27.480.081.500.221.000.15961.002096.762103.492167.2354.762299.120.891.37
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgWillapaHigh pCO2251091158610785633722031071343065732870.6135557892.0613572912543569019370253306478212921226585724.31.0030.50.362304232270241790326.821562361.19.27.480.081.500.221.000.15961.002096.762103.492167.2354.762299.120.891.37
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgWillapaHigh pCO222156683435602846211898539094829896860.5545751882.1263446542535571762723160867692689517932724.31.0030.50.362304232270241790326.821562361.19.27.480.081.500.221.000.15961.002096.762103.492167.2354.762299.120.891.37
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgWillapaHigh pCO222270690576994474105142688933241520010.6026710572.078588065348369211400722124249135944325282324.31.0030.50.362304232270241790326.821562361.19.27.480.081.500.221.000.15961.002096.762103.492167.2354.762299.120.891.37
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgWillapaHigh pCO222321761202153021203352194966911283440.5787361852.14241560995119830242661456433663421626524.31.0030.50.362304232270241790326.821562361.19.27.480.081.500.221.000.15961.002096.762103.492167.2354.762299.120.891.37
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgWillapaHigh pCO22242757234272889736753269214414554840.5406412142.062993593122004539801573627848376721710324.31.0030.50.362304232270241790326.821562361.19.27.480.081.500.221.000.15961.002096.762103.492167.2354.762299.120.891.37
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgWillapaHigh pCO22254509721447212973719439841026807800.6094884292.0053733492198311816059127037892793331905224.31.0030.50.362304232270241790326.821562361.19.27.480.081.500.221.000.15961.002096.762103.492167.2354.762299.120.891.37