TAG Meeting 2 Zachary M. Smith - PowerPoint Presentation

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TAG Meeting 2

Zachary M. SmithICPRB

1

Conference Line

: 

866-299-3188

           

Code

: 

267-985-6222

Adobe Connect

: 

https://epawebconferencing.acms.com/streamhealthworkgroup/

Meeting Website

: 

http://www.chesapeakebay.net/calendar/event/23800

Slide2

Objective

Update and refine the 2011 Chessie BIBI for Chesapeake Bay Program assessment purposes.2

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Outline

Section 1: Master Taxa List

Section 2: Site ClassificationSection 3: RarefactionSection 4: Metric Sensitivity

Section 5: Redundancy Analysis

Section 6: Scoring Protocol

Section 7: Index Resolution

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Master Taxa List

TaxaFreshwater Benthic Macroinvertebrates collected in the Chesapeake Bay watershed

222 of families (151 insect families)760 of genera (621 insect genera)

11 taxonomic ranks included (ITIS Link)

Phylum, subphylum, class, subclass, order, suborder, family, subfamily, tribe, genus, and species

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Master Taxa List

Common AttributesMunicipal Waste Tolerance

ValuesFunctional

Feeding Groups (FFG)

Habits

EPA Attributes

(

USGS 2006

,

EPA 2012

)

Respiratory Type

Voltinism

Specific Stressors

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Master Taxa List

Tolerance ValuesMean tolerance values rounded to the nearest integer

NAs not includedFFGs and HabitsThe most frequent occurring category

If max frequencies were equal the categories were concatenated (e.g. SH, CG or CL, CB)

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Tolerance Values (TV)

TV

Frequency

0

35

1

81

2

138

3

108

4

189

5

184

6

262

7

137

8

150

9311029n =1,344

Source%All Taxa% Order% Family% GenusEDAS_MD_TV80018RBP_MID_ATLANTIC_MACS_TV90417EDAS_NC_TV90120EDAS_DE_TV90019RBP_MIDWEST_OH_TV100212DC_TV11121619EDAS_RBP_TV110023EDAS_ITIS_TV1101420EDAS_KY_TV120027EDAS_PA_TV130129RBP_SOUTHEAST_NC_TV160119EDAS_WAB_TV170137EDAS_TV_FINAL2003832EDAS_WV_TV2003632EDAS_FAM_TV2003731EPA_TV36355464NYSDEC_TV53235456BIBI_TV69426979

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Functional Feeding Groups (FFG)

FFG

Frequency

CF,SC

1

CF,SH

1

CG,CF,PR,PH

1

CG,PR,PH

1

CG,SC,PR

1

PR,PA

1

SC,PR

1

SH,OM

1

SH,SC

1

CG,CF,PR2CG,SH2PR,PH2SH,PR2

CG,PR3PA3PH4CG,CF5SC,OM5PR,OM7CG,SC10CG,OM12OM16SH135CF145SC172PR423CG443Source% All Taxa% Order% Family% GenusDC_FFG1141419EDAS_KY_FFG130029EDAS_ITIS_FFG1502625EDAS_FINAL1904130EDAS_WV_FFG2103835RBP_P_FFG32213143EPA_FFG41446373NYSDEC_FFG52125455BIBI_FFG725275838

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Habits

HABIT

Frequency

BU,SK

1

CB,BU,SP

1

CB,CN,BU

1

SW,BU

1

CB,BU

2

CB,CN,SP

2

CB,SK

2

SW,SP

2

CB,CN

4

CB,SW4CN,BU5CB,SP7CN,SP7

SW,CN8BU,SP12SK15SW106CB151BU183CN232SP254Source% All Taxa% Order% Family% GenusEDAS_KY_HABIT4009DC_HABIT901218RBP_P_HABIT1541722EDAS__FINAL160235EDAS_WV_HABIT2103434HABIT_PRIM_ABBREV3803071EPA_HABIT41256274BIBI_HABIT512565829

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Unclassified Taxa

Taxa without an assigned attributeFind the percentage of taxa in each sample that are unclassifiedIf

≥ 10% of the taxa are unclassified the sample is removed from the metric calculation

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Master Taxa List

Any further comments or question regarding the master taxa list?Do you approve of the averaging tolerance values?

Do you approve of the concatenating FFGs and habits?

Are there any other tables that could be appended?

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BIBI Workflow

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Site Classification

Classes in each bioregion (7)

Reference

Near Reference

Minor Degradation

Moderate Degradation

Severe Degradation

Mixed

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Set reference standards

Standardize the impact of degradationSix Habitat Parameters∑

x < 16 = 1

∑ x

<

5 = 2

Specific

Conductivity

x > 500 = 1

x >

750

= 2

x > 1,000 = 3

pH

x < 6 or x > 8 = 1

x < 5 or x > 9 = 2

Site Classification

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Sum the degradation scores

Rate on an even scaleReference: x

= 0Near:

1 ≤ x < 3

Minor Degradation:

3

≤ x < 6

Moderate Degradation:

6

≤ x < 9

Severe Degradation:

x

≥ 9

Site Classification

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500

750

1,000

0

1

2

3

5

16

2

1

0

5

6

8

2

1

0

1

9

2

Degradation Score

Specific ConductivityRabid Habitat AssessmentpH16

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Class Gradient

100

50

0

IBI SCORE

REF

NEAR

MIN

MOD

SEV

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Biological Condition Gradient

1

4

2

3

5

6

Stressor Gradient

Biological Condition

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Biological Condition Gradient

1

4

2

3

5

6

Stressor Gradient

Biological Condition

Reference

Near Ref.

Minor Deg.

Moderate Deg.

Severe Deg.

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Metric Calculation

Metrics78 metrics from the literature

Percentage of each taxon> 1,000 metrics testedMost metrics are useless

New Metric

Common

Metric

Bioregion

% Heptageniidae

% Ephemeroptera

Piedmont

%

Systellognatha

% Plecoptera

Ridges

%

Furcatergalia

% Ephemeroptera

Ridges

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Rarefaction

Sampling without replacementrrarefy function in the Vegan package

“The random

rarefaction is made without replacement so that the variance of rarefied communities is rather related to rarefaction

proportion

than to

the

size of the sample

.”

-

Oksanen

and O’Hara

21

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Frequency

Community Composition

Rarefaction

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Family

Count

% Abundance

Rarefied % Abundance

1

EPHEMERELLIDAE

488

33.38

33

2

HYDROPSYCHIDAE

285

19.49

19

3

CHIRONOMIDAE

142

9.71

10

4

TAENIOPTERYGIDAE

1087.3975BAETIDAE94

6.4366LEPIDOSTOMATIDAE714.8657LEPTOPHLEBIIDAE654.4548TIPULIDAE654.4549HEPTAGENIIDAE543.69410CHLOROPERLIDAE191.30111ISONYCHIIDAE181.23112SPERCHONTIDAE181.23113PHILOPOTAMIDAE130.89114POLYCENTROPODIDAE130.89115EMPIDIDAE90.62116PERLODIDAE910010017CAPNIIDAE618HYDROPTILIDAE619GLOSSOSOMATIDAE420LUMBRICULIDAE421ATHERICIDAE222PERLIDAE223PSEPHENIDAE2

24

LEUCTRIDAE

1

25

ODONTOCERIDAE

1

26

PLANARIIDAE

1

27

RHYACOPHILIDAE

1

28

SIMULIIDAE

1

23

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Min = 8 taxa

Median = 15 taxa

Max = 23 taxa

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Min = 1.56

Median = 2.12Max = 2.60

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Min = 48%

Median = 69%Max = 90%True = 75%

n = 1052nr

= 100

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Rarefaction Discussion

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Metric Sensitivity

Objective: Identify metrics that best reflect a disturbance gradient

Barbour et al. 1996

Quantile Threshold Confusion Matrix Accuracy (CMA)

29

Slide30

Barbour et al. 1996

3

points

2 points

1 point

0 points

Reference

Degraded

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Slide31

Quantile Threshold

Frequency

Metric Value

2

5%

x 100

 

31

Slide32

Confusion Matrix Accuracy (CMA)

Frequency

Metric Value

15%

32

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Confusion Matrix

 

 

Predicted Class

Actual Class

Reference

Degraded

Reference

True

Reference

(

TR)

False

Degraded

(

FD)

Degraded

False

Reference (FR)

True

Degraded

(

TD)  33

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Metric Sensitivity Discussion

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Redundancy Analysis

Spearman Correlation (

≤ -0.7

or ≥ 0.7

)

Two methods:

Wilcoxon Rank Sum Test

Pairwise comparison between

Reference

and

Severe Degradation

The metric with the smaller p-value is held for further review

CMA Pairwise Gradient

Class 1

Class 2

CMA

Reference

Near Reference

73

Near Reference

Minor

Degradation64Minor DegradationModerate Degradation

57Moderate DegradationSevere Degradation77Severe DegradationReference92Mean72.636

Slide37

Redundancy Analysis

Spearman Correlation (

≤ -0.7

or ≥ 0.7

)

Two methods:

Wilcoxon Rank Sum Test

Pairwise comparison between Reference and Severe Degradation

The metric with the smaller p-value is held for further review

CMA Pairwise Gradient

Class 1

Class 2

CMA

Reference

Near Reference

73

Near Reference

Minor

Degradation

64

Minor

DegradationModerate Degradation57Moderate DegradationSevere Degradation77

Severe DegradationReference92Mean72.637

Slide38

Redundancy Analysis Discussion

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Scoring Metrics

Categorical ScoringThree categories: 1, 3, and 5

Metric decreases with degradationx > 50% = 5

25% ≤ x ≤ 50% =

3

x

< 25% =

1

Metric

increases

with degradation

x

<

50% =

5

50%

≤ x ≤

75%

=

3

x > 75%

= 1

FrequencyMetric Value15340

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Gradient Scoring

Reference Gradient vs. All GradientDecreasex ≤

5% = 0

x ≥ 95%

= 100

5% < x < 95%

Increase

x ≤

5%

=

100

x ≥

95%

=

0

5% < x < 95%

* 100

 

* 100

 

41

Slide42

Frequency

Metric Value

0

100

1 - 99

Frequency

Metric Value

0

100

1 - 99

Reference Gradient

All Gradient

42

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Threshold Gradient

Similar to the previous gradient approachesDecrease

x ≥

50%

=

100

x

≤

threshold%

=

0

threshold%

< x <

50%

Increase

x ≤

50%

= 100

x ≥

threshold

% = 050% < x < threshold% * 100  * 100 43

Slide44

Frequency

Metric Value

0

100

1 - 99

Threshold %

50%

Threshold Gradient

44

Slide45

Threshold Gradient

80

4

0

100

60

0

IBI SCORE

REF

NEAR

MIN

MOD

SEV

20

45

Slide46

Scoring Protocol Discussion

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Slide47

Metric Sensitivity Approach

Barbour et al. 1996

Confusion Matrix Accuracy (CMA)

Quantile Threshold

Categorical

Ref. Gradient

All Gradient

Scoring Approach

Threshold Gradient

Redundancy Analysis Approach

Wilcoxon Rank Sum Test

Pairwise Confusion Matrix Accuracy (CMA)

47

Slide48

Metric Sensitivity Approach

Barbour et al. 1996

Confusion Matrix Accuracy (CMA)

Quantile Threshold

Categorical

Ref. Gradient

All Gradient

Scoring Approach

Threshold Gradient

Redundancy Analysis Approach

Wilcoxon Rank Sum Test

Pairwise Confusion Matrix Accuracy (CMA)

48

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49

Slide50

Metric Sensitivity Approach

Barbour et al. 1996

Confusion Matrix Accuracy (CMA)

Quantile Threshold

Categorical

Ref. Gradient

All Gradient

Scoring Approach

Threshold Gradient

Redundancy Analysis Approach

Wilcoxon Rank Sum Test

Pairwise Confusion Matrix Accuracy (CMA)

50

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51

Slide52

Metric Sensitivity Approach

Barbour et al. 1996

Confusion Matrix Accuracy (CMA)

Quantile Threshold

Categorical

Ref. Gradient

All Gradient

Scoring Approach

Threshold Gradient

Redundancy Analysis Approach

Wilcoxon Rank Sum Test

Pairwise Confusion Matrix Accuracy (CMA)

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53

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43

1,073

445

49

6,663

415

n =

54

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43

1,073

445

49

6,663

415

n =

55

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56

43

1,073

445

49

6,663

415

n =

Slide57

57

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58

 

CMA Ref. Threshold

CMA Wilcoxon

DE Wilcoxon

Barbour Wilcoxon

1

Menhinicks

% Retreat_Trichop

% Hyrop_EPT

% Retreat_Trichop

2

HBI

%

Mod_Tol

HBI

% Mod_Tol

3

% EPT_Hydro_Baetid

% EPT

% EPT

% EPT4% Corydalidae% Corydalidae % Corydalidae % Corydalidae5% Heptageniidae% Pisciforma

% EPT_Rich_No_Tol% Pisciforma6% Isonychiidae% Isonychiidae% Isonychiidae% Isonychiidae7% Pterygota% Non_Insect% Non_Insect% Non_Insect8% Anisoptera% Odonata% Limestone% Trichop_No_Tol9% Perlidae% Systellognatha% Unionoida% Sytellognatha“Best” Metrics Piedmont

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59

 

CMA Ref. Threshold

CMA Wilcoxon

DE Wilcoxon

Barbour Wilcoxon

1

Menhinicks

%

Retreat_Trichop

% Hyrop_EPT

%

Retreat_Trichop

2

HBI

%

Mod_Tol

HBI

%

Mod_Tol

3

% EPT_Hydro_Baetid% EPT% EPT% EPT

4% Corydalidae% Corydalidae % Corydalidae % Corydalidae5% Heptageniidae% Pisciforma% EPT_Rich_No_Tol% Pisciforma6% Isonychiidae% Isonychiidae% Isonychiidae% Isonychiidae7% Pterygota% Non_Insect% Non_Insect% Non_Insect8% Anisoptera% Odonata% Limestone% Trichop_No_Tol9% Perlidae% Systellognatha% Unionoida% Sytellognatha“Best” Metrics Piedmont

Slide60

43

1,073

445

49

6,663

415

n =

60

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61

43

1,073

445

49

6,663

415

n =

Slide62

62

43

1,073

445

49

6,663

415

n =

Slide63

63

43

1,073

445

49

6,663

415

n =

Slide64

64

43

1,073

445

49

6,663

415

n =

Slide65

Binary Sensitivity

65

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66

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68

Slide69

69

Binary

Threshold CMA

Slide70

Index Resolution Type

Low ResolutionOrder

Level IndexVolunteer programs and in situ identificationModerate Resolution

Family

Level Index

Studies with limited funding and/or minimal macroinvertebrate identification experience.

70

Slide71

Index Ranks

High ResolutionGenus

Level Index

Studies with extensive funding and macroinvertebrate identification experience.Secondary indices identifying specific stressors

71

Slide72

Metric Sensitivity Approach

Barbour et al. 1996

Confusion Matrix Accuracy (CMA)

Quantile Threshold

Categorical

Ref. Gradient

All Gradient

Scoring Approach

Threshold Gradient

Redundancy Analysis Approach

Wilcoxon Rank Sum Test

Pairwise Confusion Matrix Accuracy (CMA)

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Slide73

Order

Family

Genus

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Slide74

Final Remarks

Test for agency differences within each bioregionSampling period differencesDifferences in taxa identified

Deal with unidentified taxa and unclassified taxaMissing tolerance values, FFG, or habits

Compare the 2011 indices to the 2016 indices

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