Molecular and modeling tools for 

tracking food base dynamics in 

changing environments

David A. Lytle, Professor

Angelika Kurthen, PhD student

Jared Freedman, PhD student

Oregon State University
Molecular and modeling tools for tracking food base response in changing 

environments

Project Elements and Objectives:

F.3 Invertebrate monitoring in tributaries

O.1 Does disturbance timing affect food base response?

Funding amount and source: $100,000 (AMP)

Cooperators: Oregon State University

LTEMP Resource goal:

Natural Processes-Restore, to the extent practicable, ecological patterns and 

processes within their range of natural variability, including the natural abundance, 

diversity, and genetic and ecological integrity of the plant and animal species 

native to those ecosystems.
Two goals:

1. eDN A water samples to detect and inventory 

aquatic invertebrates

2. Population models to project changes in 

aquatic invertebrate abundances due to changing 

environment and management actions

Q uagga Mussels in 

exposed algal mats at 

RM -14
Aquatic invertebrate diversity is low in the Colorado 

River below GCD
Tributaries have the potential to act as sources of 

biodiversity to the mainstem CR

Bright Angel Creek Crystal Creek Kanab Creek
But tributaries have different physico-chemical 

properties than the mainstem; can they support similar 

species?

Tapeats Creek flows into the 

Colorado
eDNA techniques allow for broad scale analysis of community 

composition; it’s a snapshot of the ecosystem state
How do invertebrate communities differ between 

tributary and mainstem reaches of the Colorado 

River within Grand Canyon?

6
eDNA water samples taken from paired tributary 

and mainstem sites within Grand Canyon

7
eDNA-derived community dataset

142bp fragment of COI 

gene amplified with 

degenerate primer set 

targeting aquatic 

invertebrates (Leese et al, 

2021)

Amplicons sequenced using 

Illumina Miseq platform

Sequences were filtered and 

clustered into OTUs using the 

R package JAMP v0.77
Taxonomic identification with BOLD database identified 

a large diversity of aquatic invertebrates

407 OTUs were ID’d to the level of order, 

spanning:

• 24 orders

• 75 families

• 84 genera

• 66 species

For contrast: Oberlin (1999) found only 42 

genera across 10 tributaries

Diptera were most common invertebrate 

order identified, with 60% of OTUs (271 

OTUs)

Limited detection of Odonata or 

Trichoptera 
harbor greater species richness

Species Richness T-test

T = 4.56, P>0.001

Stream Type 

PERMANOVA

R2: 0.206

Pseudo-F: 10.36

P>0.001

Stream Type PERMDISP

Pseudo-F: 102.4

P>0.001

Aquatic invertebrate communities in tributaries 

are distinct from those in the mainstem, and 
Downstream distance influences community 

composition in Grand Canyon tributary and 

mainstem sites

Downstream Distance 

PERMANOVA

R2: 0.139

Pseudo-F: 2.61

P>0.001

Downstream Distance 

PERMANOVA

R2: 335

Pseudo-F: 8.24

P>0.001
Key takeaways - eDNA

• Tributaries harbor distinct communities of aquatic invertebrates vs. 

mainstem habitats

• Large diversity of food base invertebrates detected with eDNA methods

• eDNA is promising for future biomonitoring of the ecosystem, although 

primer bias issues need to be addressed 

• Next: using same eDNA samples to examine fish diets and parasite 

communities
Population models for food base communities

1. C onstruct matrix population models for each relevant species

1. Parameterize with vital rates according to major event types: mortality and growth 

rates in response to HFEs, LFEs, hydropeaking, and temperature changes.

1. Use model to ask “what if” questions about future flow scenarios
Model attributes:

Temperature can affect growth, development, and 

fecundity

Flow events cause mortality but also enhance habitat

Hydropeaking affects egg establishment (for some 

species)
NZ mudsnails under future warming:

- Fecundity is temperature limited (10-27 C ; 

Bennett et al. 2015) 

- N ZMS currently winter limited

- Small winter temperature increase could 

increase mean population size
NZMS under hydropeaking:

- Relatively insensitive to hydropeaking, 

since they bear live young that can 

survive out of water >3 d
Hydropsychecaddisflies under future 

warming:

- Relatively temperature-tolerant

- Little change due to temperature alone

- Temperature-related decrease in average 

body size and fecundity
Hydropsychecaddisflies under 

hydropeaking:

- Sensitive to hydropeaking, although ther 

seems to be a threshold effect

- Remains to be seen how hydropeaking 

interacts with temperature and flow 

events
Key Takeaways - population models

• Still in development; ongoing calibration and testing

• Promising for understanding effects of temperature and flow 

scenarios (HFEs, LFEs, hydropeaking) on the invertebrate food base
Acknowledgements 

Lytle lab

Justin Hockett 

Aaron Klarenbach

Jesse Fritz

Isaac Schuman

Molly Burke - OSU

Florian Leese - University of Duisburg-Essen

USGS GCMRC

Ted Kennedy

Jeff Muehlbauer

Morgan Ford

Anya Metcalf

Chris Hunsaker - Ceiba

15
General population model 

structure