A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA
Abstract
Introduction
Material and Methods
Data Sources and Data Preparation
Distance Calculation
Clustering Optimization
Results
Taxonomic Units Based on Three-Dimensional Clustering Optimization
Alignment/alignment-free approach | Best alignment-based distance formula | Best threshold (T) | Best linkage fraction (F) | Highest MRI | Mean MRI |
---|---|---|---|---|---|
GBDP, uncorrected (λ0) | ~ | 0.27295 | 0.05 | 0.77440 | 0.74153 |
GBDP, corrected (λ1) | ~ | 0.25475/0.25735 | 0.70/0.75 | 0.80006 | 0.77958 |
GBDP, corrected (λ2) | ~ | 0.12705 | 0.00 | 0.78781 | 0.77282 |
clustalw | F84+G | 0.39070/0.40250 | 0.40/0.45 | 0.77177 | 0.73574 |
clwopt | F81+G/TamNei+G | 0.37270/0.38265/0.38330/ | 0.25/0.35/ | 0.76263 | 0.73247 |
0.38690/0.38800/0.40380/ | 0.40/0.45/ | ||||
0.40525/0.40670/0.40805/ | 0.50/0.30 | ||||
0.41165 | |||||
einsi | GTR/GTR+G/TamNei/ | 0.10300/0.10490/0.10935/ | 0.15/0.20/ | 0.75983 | 0.72110 |
TamNei+G | 0.11420/0.11615/0.12260/ | 0.25/0.30/ | |||
0.12125/0.12340/0.12955/ | 0.35/0.40/ | ||||
0.13600/0.13860/0.14860/ | 0.10 | ||||
0.11355/0.11550/0.12190/ | |||||
0.11560/0.12145/0.12785/ | |||||
0.13360/0.13650/0.14565000 | |||||
ginsi | GTR+G | 0.70360 | 1.00 | 0.76705 | 0.72616 |
kalign | RAxML/F81/F81+G/F84/ | 0.06205/0.05910/0.06410/ | 0.00 | 0.77756 | 0.75664 |
F84+G/GTR/GTR+G/JC/ | 0.05915/0.06420/0.05950/ | ||||
JC+G/K2P/K2P+G/K3P/ | 0.06560/0.06405/0.05920/ | ||||
K3P+G/LogDet/TamNei/ | 0.06430/0.05785/0.05680/ | ||||
TamNei+G | 0.064450 | ||||
linsi | GTR/GTR+G/LogDet/ | 0.12520/0.12625/0.12955/ | 0.35/0.40/ | 0.73862 | 0.71920 |
TamNei/TamNei+G | 0.15285/0.15495/0.15805/ | 0.45 | |||
0.12365/0.12465/0.12440/ | |||||
0.12525/0.14930/0.15090/ | |||||
0.15540000 | |||||
mafft | P/TamNei | 0.10545/0.12495/0.131550 | 0.25/0.35/ | 0.76322 | 0.73867 |
0.40 | |||||
muscle | TamNei | 0.17965 | 0.15 | 0.74915 | 0.70428 |
nralign | F81/F84/GTR+G/JC/ | 0.16595/0.16600/0.21925/ | 0.15 | 0.76217 | 0.71718 |
JC+G | 0.16575/0.20845 | ||||
poa | F81 +G/JC/JC+G/K2P/ | 0.16755/0.13815/0.16710/ | 0.10 | 0.76758 | 0.73450 |
K2P+G/K3P/TamNei+G | 0.13830/0.16765/0.13840/ | ||||
0.16870 | |||||
poaglo | TamNei | 0.13610 | 0.10 | 0.78435 | 0.71880 |
Assigned morphotaxon (accession nos., individuals)a | Original cluster number | Associated TU | Status |
---|---|---|---|
Globigerina bulloides | 17 | BUL | OK |
G. indet. sp. U80793 | 17 | BUL | Identified using clustering |
G. indet. sp. from Okinawa trough | 17 | BUL | Identified using clustering |
Indiv. R043, determined as G. bullides; clone 1 | 5 | [Cluster 5] | Missing data (‘N’) artefactb |
Indiv. R043, determined as G. bulloides; clone 2 | 12 | SIP-A | Possible misdetermination |
G. falconensis | 3 | FAL | Few data |
Globigerinella calida Z83960 | 12 | SIP-A | Possible misdetermination78 |
G. siphonifera AJ251213, AJ390578, AJ390580 | 20 | SIP-B | Includes G. siphonifera type IV41 |
G. siphonifera, all other sequences | 12 | SIP-A | Includes G. siphonifera types I, IIa, IIb/III40,41,78,79 |
Undetermined spinose individual P125 | 12 | SIP-A | Identified using clustering |
Undetermined spinose individual P155 | 20 | SIP-B | Identified using clustering |
Globigerinita glutinata | 22 | GLU | OK |
G. uvula AF387173 | 4 | UVU-A | Provisional, very few data |
Two small individuals, possibly G. uvula28 | 2 | UVU-B | Provisional, few data |
Globigerinoides conglobatus | 9 | CON | Very few data |
G. ruber ‘pink’ or ‘white’ | 8 | RUB | Synonym of G. ruber types I and P73,79,80 |
G. ruber ‘white’ AF102230 | 9 | CON | Synonym of G. ruber type II40,73 |
G. sacculifer Z69600 | 9 | CON | Known misnomer81 |
G. sacculifer, all other sequences | 7 | SAC | OK |
Globorotalia crassaformis AY453134 | 13 | MAC-A | Possible misdetermination (Kimoto and Tsuchiya, unpublished; available in GenBank |
G. inflata | 13 | MAC-A | OK |
G. hirsuta indiv. R002 clone 09 | 1 | [Cluster 1] | Missing data (‘N’) artefactb |
G. hirsuta, all other sequences | 18 | HIR | OK |
R021, undetermined globorotaliid (possibly G. scitula) | 18 | HIR | Identified using clustering |
R034, undetermined globorotaliid | 14 | MAC-B | Could be first true G. crassaformis; more data needed |
G. menardii | 11 | MEN | Very few data |
G. truncatulinoides | 19 | TRU | OK |
Hastigerina pelagica Z83958 and individuals R022/P101 | 6 | PEL-A | OK28 |
H. pelagica, remaining individuals | 21 | PEL-B | OK28 |
Neogloboquadrina dutertrei | 14 | MAC-B | Few data |
N. incompta, including revised N. pachyderma | 16 | INC | Synonym of N. pachyderma dextral; type R;72N. pachyderma dextral types I, II82 |
N. pachyderma | 13 | MAC-A | Synonym of N. pachyderma type I;69N. pachyderma sinistral types I–VII72,74 |
Orbulina spec., O. universa | 10 | ORB | Synonym of Orbulina mediterranean, caribian, Sargasso type78,80 |
Pulleniatina obliquiloculata | 14 | MAC-B | Very few data |
Turborotalita quinqueloba AF250116 | 0 | QUI-A | Very few data |
T. quinqueloba, all other sequences | 15 | QUI-B | Few data |
Robustness of Clustering Optimization
Discussion
Clustering Optimization for Molecular Taxonomy
Implications for a Taxonomic Synopsis in Planktonic Foraminifera
Conclusion
Author Contributions
Disclosures
Abbreviations
- GBDP
- Gen(om)e BLAST distance phylogeny
- ML
- maximum likelihood
- MSA
- multiple sequence alignment
- PF
- planktonic foraminifera
- TU
- taxonomic unit.
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