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Data consolidation rules
The pigment ratio database is primarily based on peer-review publications, with additions of data from other publication type (reports, books, etc) when available. It can also contain unpublished data. Publication type / status is included as metadata.
To see how those rules are applied in practice, see the Import description.
Frequently, published material contains only a synthesis of the results, for example, providing quantitative data only for the most abundant or most relevant pigments for the study in question. Other pigments receive qualitative information only or no explicit information. Common qualitative information are "present in some taxa" and "trace amounts". This consolidation adds absences (zeros) based on known absences from pigment distributions among taxonomic and pigment groups (provided table on the aux directory) as well as attributes measurements to individual pigments when HPLC method does not resolve them (based on pigment distribution). Pigments present in some species or in trace amounts are left as NA is no other information is provided on the source. Additionally, if the method resolves diagnostic pigments (e.g., DVChl a, Perid) or diagnostic pigment between pigment groups of taxonomic groups (e.g., Pras in Prasinophytes, Myxo in Cyanobacteria, Chl c3 in Diatoms), but the pigment is not reported, is assumed to be zero. A comprehensive list of pigments is included, excluding however pigments without proper correspondence between HPLC systems (e.g., pigments described with the qualifier "-like") and degradation products.
The minimum information in the database is that provided directly in the source publications, with addition of "pigment group", to be described later. All other parameter fields included in this database that are not directly provided in the publication may be added (with help of the community). Those parameters can be useful when subsetting the data before calculation of descriptive statistics and include ecological and taxonomy information, described below.
The pigment group approach recognize that not all organisms in a given higher taxa have the same pigment associations. For example, for chemical taxonomy applications, Higgins et al. 2011 provide a series of pigment ratio matrix for specific pigment groups within taxonomic groups. Those are based on the pigment group description of Jeffrey et al., 2011. For example, for dinoflagellates, pigment associations containing peridinin are the most common (DINO_1, in Jeffrey et al., 2011), but other chloroplast types are possible that do not have peridinin, and can even present chlorophyll b. A priori pigment group is provided with the database, inferred from the pigment group descriptions in Jeffrey et al., 2011. However, pigment groups separable from the available pigments resolved by the HPLC of a given user may be recalculated by ordination / cluster analysis. R scripts to automate this process for the most common HPLC methods will be made available in a future version of this database.
From the perspective of chemical taxonomy, generally only higher taxa information is relevant (e.g., Division and Class). However, species identification or even full taxonomic description can be very useful, for example, when building a initial pigment ratio for a specific location, when the taxonomic information can serve as rough guide of the pigment groups (sensu Jeffrey et al., 2011) that should be present in the samples. It can also help to match ecological information to subset the data before descriptive statistics are calculated. To provide a robust support for the taxonomic information in light of the evolving taxonomy of many groups, numerical identifications in taxonomic databases can be added to each species. Those are the AphiaID of WORMS and the species number of EOL. During this process, the species name should be updated to currently accepted denominations. The original names reported in the source publication are kept to facilitate merging with other databases (e.g., importing full pigment matrices from authors).
To make the database more specific, a small set of ecological metadata is potentially included. This include "Living" mode (e.g., planktonic, benthic), "Habitat" (e.g., marine, freshwater, brackish water), and an indication if the species is boom-forming and if has the capability of producing toxins.
The citation to the source of data. If unpublished, the format is "LastName, unpublished". The full references are provided in a separate file. For unpublished data, it includes the contact and research institute of the contributor. It is obligatory parameter.
Taxonomic group broadly associated with Class rank. For some groups this will be Division rank. Those groups form the primary taxonomic identity to define pigment groups (shown in parenthesis below). The phylogenetic relations of Prasinophytes is still evolving and the former Class has been subdivided in 8 classes listed below. This additional taxonomic information may be relevant for reorganizing pigment groups (e.g., Latasa et al., 2004) and the taxonomic group of Prasinophyte species should be listed as Prasinophytes_X, were X is the class now associated with the clade. It is obligatory parameter. Accepted values are (Jeffrey et al., 2011):
- Bolidophytes (BOLIDO-1);
- Chlorarachniophytes (CHLORARACH_1);
- Chlorophytes (CHLORO_1, CHLORO_2);
- Chrysophytes (CHRYSO_1);
- Cryptomonads (CRYPTO_1);
- Cyanobacteria (CYANO_1, CYANO_2, CYANO_3, CYANO_4, CYANO_5)
- Diatoms (DIATO_1, DIATO_2, DIATO_3);
- Dictyophytes (DICTYO_1);
- Dinoflagellates (DINO_1, DINO_2, DINO_3, DINO_4, DINO_5);
- Euglenophytes (EUGLENO_1);
- Eustigmatophytes (EUSTIG_1);
- Glaucocystophytes (GLAUCO_1);
- Mesostigmatophytes (MESOSTIG_1)
- Pavlovophytes (HAPTO_12);
- Pelagophytes (PELAGO_1);
- Phaeothamniophytes (PHAEOTHAM_1);
- Pinguiophytes (PINGUIO_1);
- Prasinophytes (PRASINO_1A, PRASINO_1B, PRASINO_2A, PRASINO_2B, PRASINO_3A, PRASINO_3B);
- Pyramimonadophyceae (Prasinophyte Clade I);
- Mamiellophyceae (Prasinophyte Clade II);
- Nephroselmidophyceae (Prasinophyte Clade III);
- Chlorodendrophyceae (Prasinophyte Clade IV);
- Pycnococcaceae (Prasinophyte Clade V);
- Palmophyllophyceae (Prasinophyte Clade VI);
- Chloropicophyceae (Prasinophyte Clade VII A and VII B);
- Picocystophyceae (Prasinophyte Clade VII C);
- Prymnesiophytes (HAPTO_3, HAPTO_4, HAPTO_4, HAPTO_6, HAPTO_7, HAPTO_8);
- Raphidophytes (RAPHIDO_1);
- Rhodophyta (RHODO_1);
- Synurophytes (SYNURO_1);
- Trebouxiophytes (TREBOUXIO_1);
- Xanthophytes (XANTHO_1);
Species name reported in the source document. It is kept for verification against the original document.
The currently accepted species name. This is retrieved by searching the WoRMS database by the reported name of the species in the source document. It is possible to use the WoRMS API to query from command line. It is an optional field and if not validated will contain NA.
The codes associated with the species in WoRMS (AphiaID) and EOL (EOLID).
One of planktonic, benthic, symbiont or macroalgae (possibly part of the plankton in one stage of the life cycle). This information is gathered from WoRMS or EOL when available. It is an optional field and if not validated will contain NA.
The most common habitat. One of: marine, brackish, freshwater. This information is gathered from WoRMS or EOL when available. It is an optional field and if not validated will contain NA.
Logical (TRUE or FALSE), indicating if the species has been observed to form blooms. This information is gathered from the source publication, WoRMS or EOL when available. It is an optional field and if not validated will contain NA.
Logical (TRUE or FALSE), indicating if species is known to produce toxins. This information is gathered from the source publication, WoRMS, EOL or the IOC-UNESCO Taxonomic Reference List of Harmful Micro Algae. It is an optional field and if not validated will contain NA.
Irradiance intensity during cultivation. Three levels are used:
- Low light (LL): < 30 µmol quanta m-2 s-1;
- Medium light (ML): 30-130 µmol quanta m-2 s-1;
- High light (HL): > 130 µmol quanta m-2 s-1.
The pigment group that the organism represent. This classification follows the descriptions of Jeffrey et al., (2011) which is simplified in Higgins et al (2011) considering application in chemical taxonomy. For most groups listed in "Taxonomic Group", there is only one pigment group. Below are listed the diagnostic pigment presence / absence for the taxonomic groups with more than one pigment group. Note that in the case of Haptophytes, the diversity of pigment groups identified in Zapata et al. (2004) (reproduced in Jeffrey et al., 2011) had to be reduced due to consolidation rules (which defines pigments included in the database). Based on the pigment ratios for those Haptophyte pigment groups as described in Zapata et al. (2004), the merge results only in loss of resolution, not an artificial increase in variance of pigment ratios. If it is not possible to classify which variant, classification is "NAME_X", e.g., HAPTO_X. Abbreviations are listed in the pigment list.
Cyanobacteria:
- CYANO_1: Presence of Myxo;
- CYANO_2: Presence only of Chl a, β,β-Car and Zea (traces of MgDVP);
- CYANO_3: Absence of Myxo, presence of Chl b;
- CYANO_4: Absence of Chl a and presence of DVChl a, DVChl b, β,ε-Car;
- CYANO_5: Presence of Chl d;
Chlorophytes:
- CHLORO_1: Base type (absence of Pras and Siph);
- CHLORO_2: Presence of Pras and Siph;
Prasinophytes:
- PRASINO_1A: Base type (absence of Pras, Siph, Loro);
- PRASINO_2B: Presence of Allo (Lopes dos Santos et al., 2017)
- PRASINO_2A: Presence of Loro;
- PRASINO_2B: Presence of Siph;
- PRASINO_3A: Presence of Pras;
- PRASINO_3B: Presence of Pras, Micral and/or Uri;
Diatoms:
- DIATO_1: Presence of Chl c1 and presence of Chl c2;
- DIATO_2: Absence of Chl c1 and presence of Chl c3;
- DIATO_3: Presence of Chl c1, Chl c2 and Chl c3;
Dinoflagellates:
- DINO_1: Presence of Perid;
- DINO_2: Absence of Perid, presence of Chl c3 and Fuco;
- DINO_3: Absence of Perid, presence of Chl c1 and Fuco;
- DINO_4: Absence of Perid, presence of Allo;
- DINO_5: Absence of Perid and Chl c2, presence of Chl b;
Haptophytes (HAPTO_1 merged with HAPTO_2 due to consolidation rules):
- HAPTO_12: Of Chl _c_s, only present Chl c1, Chl c2 and MgDVP;
- HAPTO_3: HAPTO_12 + Chl c2-MGDG[18/14];
- HAPTO_4: HAPTO_3 + Chl c3;
- HAPTO_5: HAPTO_4 + Hex_kFuco;
- HAPTO_6: Presence of MVChl c3 and absence of Chl c1;
- HAPTO_7: HAPTO_4, absence of Chl c1 with presence of Chl c2-MGDG[14/14];
- HAPTO_8: The same as HAPTO_7, but without Chl c2-MGDG[14/14];
The next set of parameters are individual pigments and some aggregates defined in systems with lower pigment resolution, depending on HPLC system (see pigment resolution). The list of included pigments, their abbreviations and alphanumeric codes is available here. A small subset of the know pigments is included, and in particular, pigments lacking proper identification are not included.
Pigment ratios are provided in two formats: as mass rations and as molar ratios. Conversions, when importing a database, are made using the molecular weight of the pigments available in the data sheets of Jeffrey et al. (1997) and Egeland et al. (2011). The molar weight of the pigments included in this database is available as a separate file in the aux directory.
The conversion from molar ratios to mass ratios is made by multiplication of the pigment molar ratios by the molar weight ratio Mwk / MwChl a, where "k" is a given pigment. The opposite conversion, from mass to molar ratios is likewise done by multiplication with the inverse of the previous molar weight ratio, MwChl a / Mwk.