Diatom Intercalibration Workshops

Diatom Intercalibration Workshops

4 meetings: attended by Annie, Elinor, Kaarina

Dave Ryves guest appearance

Issues covered: ID notes for 100 common taxa

Clumping of ‘problem’ species complexes

Excluded taxa

Cross counting exercise

Clumping of ‘problem’ species complexes

Planothidium delicatulum agg.: P. delicatulum, P. haukianum, P. septentrionalis, P. engelbrechtii

Fragilaria elliptica agg.: Staurosira elliptica (1&2), S. punctiformis, Staurosirella sopotensis, Pseudostaurosira perminuta, P. zeillerii, Opephora krumbeinii, Fragilaria neoelliptica, F. sopotensis, F. guenter-grassii

Tabularia fasciculata agg.: T. affine, T. laevis, T. fasiculata, T. tabulata, T. waerneii

Nitzschia frustulum agg.: N. amphibia, N. amphibia f. rostrata, N. frustulum, N. inconspicua, N. liebtruthii, N. liebtruthii v. major

Complexes continued

Excluded taxa

Chaetoceros spp. resting spores as identification to species level not possible.

Chaeotoceros spp. vegetative cells, Skeletonema costatum and Rhizosolenia spp. spines as preservation in sediments is uneven.

Cross Counting Exercise

All 3 diatomists within 5% of each others counts after the exercise finished.

(We weren’t after the first attempt!)

Still To Do

Authorities and references for MOLTEN taxa

Agreement on data-base images

Transfer Function Requirements

Unimodal models

The under-lying taxa-response should predominantly be unimodal

Use Detrended Canonical Correspondence Analysis:gradient lengths greater than 2 have many taxa showing a unimodal response,less than 1 and no taxa will have a unimodal reponse

Variables to be reconstructed should explain a significant (and unique) portion of the variance in the diatom data: CCA (and partial CCA) tested by Monte Carlo permutation tests are used to determine this.

Dutch training set

30 sites within country

Sylt/Seine samples

308 taxa in total

53 taxa with 1% abundance in 2 or more samples

Thalassiosira pseudonana (42%), Delphineis surirella (29%) and Cymatosira belgica (20%) were among the most widespread and abundant taxa.

-0.5 3.0

-0.5

2.0

BOCHTTND

DREISRLODSGT

SOELKK

VLISGSVH

YERSKVWT

DCA Gradient length 2.5 (without SOELKK 1.8)

DCCA on TN gradient 0.7

DCA

Adding Western Danish samples gave only small improvement:

DCA gradient 2.3


Dutch data set DCA (26 sites & 54 taxa)

Dutch diatom data

-1 4

-35

AcnMinAG

CerPel

Cocneot

CycCho

CycSmiA

CymtBel

DelSur

DipAes

FalTen

FraEllAG

NavFenAF

NavFla

NavPhy

NavPor2C

NitAeq

NitAmeC

NitPal

ParaSul

PlapCra

PlaVan

RhapAmp

SMAGIV

StalPin

TabFasAG

ThaInc

ThanNit

ThaOes

-2 4

-34

AcnMinAG

CerPel

CycCho

CycSmiA

CymtBelDelSur

DipAes

FalTen

FraEllAG

NavFenAF

NavFla

NavPhy

NitAeq

NitAmeC

NitPal

ParaSul

PlapCra

PlaVanRhapAmp

SMAGIV

StalPin

TabFasAG

Tha11A

ThaInc

ThanNit

ThaOes

All sites

SOELKK removedDCA

DCA

Gradient length 2.5 Gradient length 1.8

-0.8 0.8

-0.8

0.8

Ach11A

AcnMinAG

AmpCof

AmpHel

AnaBal

CatAdh

Cocneot

CocPel

CycCho

CycSmiA

CymtBelDelSur

DimMin

DipAes

FalCry

FalTen

FraEllAG

NavFenAF

NavPerm

NavSubm

NitAeq

NitAmeC

NitFruAG

OpeHor

OpeMut

ParaSul

PlaBro

PlanDelG

PlapCra

PlaVan

RhapAmp

StalPin

TabFasAG

ThaInc

ThanNit

ThaOes

ThaPro

ThaPseu

Unk33A

depth

salinity

PO4

TP

NOx

NH4

TNSiO3

Chl-a

secchi

Dutch data set RDA (SOELKK removed)

Linear version of CCA

Interpret in same way

Significance testing with Monte Carlo permutation tests indicated that only NH4 had a significant relationship to distribution of diatom taxa.

C1 C2 C3RMSE 0.08 0.05 0.03R2 0.67 0.87 0.93RMSEP 0.12 0.17 0.18Boot_R2 0.38 0.15 0.08

PLS on NH4 (DCCA gradient length 1.3)

Dutch training set Performance

Danish training set

91 sites

508 taxa in total

152 taxa with 1% abundance or more in 2 or more samples

Opephora mutabilis (22%), Fragilaria elliptica agg. (26%) and Thalassiosira sp. 1A (55%) were among the most frequent and abundant taxa.

Danish site DCA

-0.5 3.5

-0.5

3.0

FRB1939FYN65053

FYN67053 NJYD10NJYJ10

NJYJ2

RIB16101

RIB16212

RKB1RKB2

RKB23

ROS52

ROS55

ROS60

ROS62

SJY20

SJY3

STR32051

STR81006

STR82008

STR91008

VEJ5367

VIB37021VIB37081

VIB37131

VIB37201

VIB37221

VIB37281

Shallow, sandy, saline

Deep

Shallow, brackish

Gradient length 3.1

-1.5 2.5

-1.5

1.5

depth

salinity

PO4

TPNH4_N

TNchla

FYN63044

RIB16103

RIB16212

RKB2

RKB23

ROS55STR13005

VIB37021

VSJ44011

CCADCA gradient length 3.1


Variables in BLUE are significant in forward selection

Danish data set CCA (91 sites & 152 taxa)

Danish Diatom CCA

-1.0 1.0

-1.0

1.0

Ach11A

AchAmo

AcnMinAG

AmpHel

BirSpp

CosAst

CycMen

CycsDub

CycStrAG

CymtBelCymThu

DelSur

DipPar

Fra1A

FraAmi

FraGeo

FraNeop

FrapCyl

GompExi1

GyrPei

MarAto

MelMon

Nav12A

Nav4A

NavAbo

NavCin

NavIndC

NavJae

NavLacC

NavMens

NavPerm

NavPhy

NavPor2CNitComt

NitDistC

NitFruAG

PauTae

PlaBroPlaVan

PsenSerC

StaCon1

StalLap

StalPin

SteHan

Tha1A

Tha3A

Tha4A

ThaAng

ThaBalThaDec

ThaEccThanNit

ThaPseu

Unk1A

UnkCen1A

depth

salinity

PO4

TN

Nutrient variables (with exception of PO4) are colinear.

C1 C2 C3RMSE 0.14 0.11 0.089R2 0.69 0.81 0.88RMSEP 0.18 0.16 0.17Boot_R2 0.56 0.65 0.66

Danish predicted vs obs TN

2.25 2.40 2.55 2.70 2.85 3.00 3.15 3.30 3.45 3.60

2.25

2.40

2.55

2.70

2.85

3.00

3.15

3.30

3.45

3.60

observed TN (log µg/l)

pre

dic

ted

TN

(lo

g µ

g/l)

predicted vs observed TN for Danish TS scaled by salinity

-1.0 1.0

-1.0

1.0

depth

salinity

PO4_P

TP NOx_NNH4_N

TNSiO3_Si

chla

sw_Astol

sw_Bytte

sw_Kl8

sw_Mella

sw_Rev2

sw_Va10

DCA Gradient length 3.7

DCCA on TN gradient 2.5 CCA

Swedish Data Set (30 sites & 75 taxa)

2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 3.0 3.1

2.2

2.3

2.4

2.5

2.6

2.7

2.8

2.9

3.0

3.1

sw_Mel la

sw_Sjosa

sw_Stads

observed log TN

pre

dic

ted

log

TN

Bootstrap WAPLS 2 TN vs observed TN points scaled by salinity

C1 C2 C3R2 0.76 0.86 0.94 RMSE 0.085 0.065 0.044Boot_R2 0.60 0.63 0.65RMSEP 0.12 0.12 0.12

Swedish predicted vs Obs TN

-0.6 1.0

-1.0

1.0

depthsalinity

PO4_P

TP

NOx_N

NH4_N

TN

SiO3_Si

chloroph

secchi

fi_23

fi_39

fi_43

fi_46

fi_47

fi_5

fi_60

fi_62

DCA gradient length 2.8


DCCA on TP gradient 1.9

CCA

Finnish Data Set (55 samples & 73 taxa)

Finnish predicted vs obs TN

2.5 2.6 2.7 2.8 2.9 3.0 3.1 3.2 3.3 3.4

2.5

2.6

2.7

2.8

2.9

3.0

3.1

3.2

3.3

3.4

fi_11

fi_23

fi_28

fi_33

fi_34

fi_35

fi_46

fi_47

fi_59

fi_60


pre

dic

ted

TN

(lo

g µ

g/l)

Model performance

C1 C2 C3

RMSE 0.094 0.076 0.063

R2 0.69 0.79 0.86

RMSEP 0.13 0.13 0.14

Boot_R2 0.48 0.51 0.48

Model performance (fi_46 removed)

C1 C2 C3

RMSE 0.084 0.066 0.055

R2 0.75 0.85 0.89

RMSEP 0.13 0.12 0.12

Boot_R2 0.56 0.60 0.62

1.00 1.25 1.50 1.75 2.00 2.25

1.00

1.25

1.50

1.75

2.00

2.25

observed TP (log µg/l)

pre

dic

ted

TP

(lo

g µ

g/l)

Finnish predicted vs obs TP

Model performance

C1 C2 C3

RMSE 0.083 0.073 0.066

R2 0.67 0.74 0.79

RMSEP 0.11 0.10 0.11

Boot_R2 0.53 0.59 0.61

-1.0 5.0

-0.5

3.5

All Sites DCA

Open shallow sandy

Open deep muddy

Baltic

Finnish Danish Dutch Swedish

CCA DCA gradient length 4.13



DCCA on salinity gradient 3.0

CCA with forward selection indicated ALL variables to be significant

MOLTEN Data Set CCA (202 sites & 234 taxa)

-0.6 1.0

-0.6

1.0

depth

salinity

PO4_P

TP

NOx_N

NH4_N

TN

chla

fi_23

fi_33

fi_47

fi_5

fi_62

sw_B1

sw_K3v

sw_Mella

sw_OVF52

sw_Rev2

sw_Sjosa

sw_Stads

sw_Va10

CCA

DCA gradient length 3.3



Forward selection indicated ALL variables to be significant, those in BLUE explained highest total variance

East coast Sweden and Finland

Baltic Data Set CCA (75 sites & 86 taxa)

2.40 2.55 2.70 2.85 3.00 3.15 3.30 3.45 3.60

2.40

2.55

2.70

2.85

3.00

3.15

3.30

3.45

3.60


pre

dic

ted

TN

(lo

g µ

g/l)

Model performance

C1 C2 C3

RMSE 0.10 0.08 0.07

R2 0.70 0.79 0.84

RMSEP 0.13 0.13 0.14

Boot_R2 0.55 0.57 0.54

Baltic Predicted vs obs TN

Baltic predicted vs obs TP

1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 2.0 2.1

1.1

1.3

1.5

1.7

1.9

2.1

observed TP (log µg/l)

pre

dic

ted

TP

(lo

g µ

g/l)

Model performance

C1 C2 C3

RMSE 0.10 0.08 0.07

R2 0.61 0.73 0.77

RMSEP 0.12 0.12 0.13

Boot_R2 0.49 0.51 0.52

-1.0 1.0

-1.0

1.0

depth

salinity

PO4_P

TP

NOx_N

NH4_N

TN

chla

NJYJ2

RIB16212

RKB23

ROS52

ROS55

sw_Bytte

sw_N7

VSJ44011

CCADCA gradient length 3.1



DCCA on salinity 2.1

Danish with Swedish west coast (101sites & 163 taxa)

-1.0 1.0

-1.0

1.0

depth

salinity

PO4_P

TP

NOx_N

NH4_NTN

chla

NJYJ10

NJYM3

ROS52

ROS55

SJYKFF2

sw_Astol

sw_Bjork

sw_Byfjo

sw_Byttesw_EAlv sw_Galte

sw_N5

sw_N6

sw_N7

VSJ10002

CCA DCA gradient length 2.9



DCCA on salinity gradient 2.0

Danish and Swedish West Coast > 10m CCA (56 sites & 121 taxa)

Documents

Diatom Intercalibration Workshops