Stream Habitat and Biota in Karst Landscapes

Comparing Upstream and Downstream sites based on stream, fish, and invertebrate variables

Background

Mundahl & Mundahl (2022), Ecological Processes

Compare upstream vs downstream sites using NMDS ordination

Focus:

  • Stream habitat

  • Fish species abundance

  • Invertebrates species abundance

Data

  • Stream: 18 variables (% , averages)

  • Fish: 19 species counts

  • Invertebrates: 39 species counts

# A tibble: 6 × 6
   Site `Stream Width` `Mean Depth` `Mean CV` `% Fines` Embeddedness
  <dbl>          <dbl>        <dbl>     <dbl>     <dbl>        <dbl>
1     1            2.6           26        14        46            5
2     2            2.3           45         6        67            5
3     3            4             41         7        58            4
4     4            5.2           48         2        68            5
5     5            4.3           47        14        87            5
6     6            4.1           24        29        56            5

Methods

Data Setup

  • Grouped sites into Upstream (1–12) and Downstream (13–22)

  • Split data into

    • Stream (18 variables),
    • Fish (19 species), and
    • Invertebrates (39 species)

Ordination

Ran NMDS for each domain using appropriate distance metrics:

  • Gower for stream (% and averages)

  • Bray-Curtis for fish and invertebrate abundance

All stress values < 0.2 → valid ordinations

Anaysis

Used envfit to regress variables onto NMDS space.

Filtered meaningful variables(p_val< 0.05).

Filtered arrows for plotting based on R² thresholds:

  • Stream > 0.5

  • Fish > 0.4

  • Invertebrate > 0.3

R² thresholds were somewhat arbitrary but kept to retain variables with ecological meaning and interpretive value.

Stream NMDS Biplot

  • Upstream and Downstream sites are clearly separated.

  • Ellipses show minimal overlap, confirming strong differentiation.

  • Key drivers: Stream Width, Buffer Width, % Fines, Embeddedness.

Fish NMDS Biplot

  • Distinct clustering of Upstream vs Downstream sites.

  • No ellipse overlap highlights strong ecological separation.

  • Influential species include Brown Trout, Blacknose Dace, Creek Chub, and Slimy Sculpin.

Invertebrates NMDS Biplot

  • Upstream and Downstream sites show limited clustering.

  • Significant ellipse overlap suggests subtle ecological separation.

  • Key indicator taxa include Baetis, Simulium, Hydropsyche, and Caenis.

wilcoxon test

  • Focuses on NMDS-important variables only

  • Use Wilcoxon tests to find key variables that show significant differences between Upstream and Downstream sites.

Stream
Variable p_value
Stream Width 0.0000865
% Fines 0.0013709
Embeddedness 0.0097236
Buffer Width 0.0035998
Fish
Variable p_value
Creek Chub 0.0000770
Central Stoneroller 0.0001224
Brown Trout 0.0001764
Slimy Sculpin 0.0075564
Invertebrate
Variable p_value
Caenis 0.0024967
Baetis 0.0008543
Stenonema 0.0370432
Hydropsyche 0.0091010
Cheumatopsyche 0.0040332
Simulium 0.0001354

Significant Stream variables

  • % Fines and Embeddedness are high at Upstream sites and lower at Downstream.

  • Downstream sites feature wider buffers and stream channels.

Significant Fish variables

  • Brown Trout and Slimy Sculpin are more abundant at Downstream sites.

  • Creek Chub is more abundant at Upstream sites.

Significant Invertebrates variables

  • Baetis, Simulium, and Hydropsyche are more abundant at Downstream sites.

  • Stenonema, Cheumatopsyche, and Caenis are more abundant at Upstream sites.

Summary

  • Yes, based on NMDS biplots upstream and downstream sites differ with respect to the variables measured.

  • Fish variables show the least overlap between upstream and downstream.

  • Downstream: Higher levels of % Fines and Embeddedness (stream), Brown Trout and Slimy Sculpin (fish), and Baetis, Simulium, Hydropsyche (invertebrates).

  • Upstream: Wider buffers and stream channels, more Creek Chub and Stenonema (fish), and more Cheumatopsyche and Caenis (invertebrates).